The story starts from the description of life of Lena Grove. She is a young woman whose parents have died recently. She moves to live with her brother. There she meets a man named Lucas Burch and falls in love with him. It seems that is mutual, but Lucas doesn’t make her a proposal. When it becomes obvious that Lena is pregnant, Lucas hastily goes away, saying that he will send for Lena when he finds a good job and place to settle down. Lena waits for him for some months, but there is no news from her beloved. Deciding that something bad could happen to him, the woman, while pregnant, walks the way he told her he would use, from Alabama to Mississippi, asking about Lucas Burch everywhere. Finally she finds a trace: a rumor that the man looking like Lucas can be in Jefferson. Lena continues her journey there. When she arrives the town she sees that the old plantation building is on fire. She learns that it was the house of Joanna Burden and it was supposedly a murder. Joe Christmas, a black person who lived in an old cabin that was used for slaves before, was accused of it. There were no evidences, but the fact that Joe and Joanna were lovers was enough for the crowd. They care more about such a “horrible” adultery of white woman and black man than about the actual deceased Joanna.
The narrative shifts to the events three year prior to this: a man named Byron Bunch is working on the planing mill in Jefferson. He sees Joe Christmas, who is looking for work and is pretty exhausted - he got one refusal after another just because he is black. Byron hires him. Later the man named Joe Brown also comes searching for work and is hired too. Christmas and Brown work together a lot and seem to befriend each other, but none of the other people is sure about the nature of their relationship. Brown learns that once Joe Christmas was the owner of a whiskey distillery and - in a strange way - still has whiskey from it. He and Brown form a partnership: Christmas delivers whiskey and Brown sells it to the customers. Soon they both quit their job on the planing mill and go to rent old cabins on the ground of Miss Joanna Burden, their landlady and owner of the plantation. Joanna’s family moved to Jefferson from the North during Reconstruction, so she is a Yankee - that means a person who sees nothing wrong in treating people of color as equals.
The story returns to the present time. Byron is still working on the mill and now he sees Lena Grove and hears she is looking for Lucas Burch. He starts a conversation, because he knows Lucas and because he likes Lena. But during the conversation he learns that it was actually Lucas who impregnated her and she still loves him so much she walked such a long way while pregnant. During the talk Byron lets the fact that Joe Brown is actually Lucas Burch slip and is very unhappy about it, because he was already thinking about courting Lena.
The narrative again turns to the story of another inhabitant of Jefferson - Reverend Gail Hightower, who moved there long ago with his family and became a priest in Jefferson Presbyterian church. Hightower’s wife, though, misses her family and frequently leaves the town to visit her relatives. But soon the people start gossiping that Mrs. Hightower visits someone else in Memphis, not her family. The whole town is discussing the rebellious woman and her potential interest in Memphis. Once she even gets jailed and soon released to return to her husband and never do this again. However, she continues to go to Memphis and once dies because of an incident - falling from the hotel window. She was in the hotel with another man and they were registered as husband and wife. The size of scandal makes Hightower to leave his position of a minister. The townsfolk also actively tries to get him out at all, but Hightower refuses to move. Gradually the rumors are toned down, but Hightower is forever left an exile in the town.
In the present time Byron visits the former priest and tells him what happened with Burden house. It appears that Joanna’s throat was slit before the house was set on fire to cover the traces of the murder. Brown was interrogated by the local sheriff and told him that the only one who could be in the house was Christmas, Joanna’s lover. The idea of a black man sleeping with white woman shocked the sheriff so much that he questioned no more. It is unclear how much truth is there in Brown’s words, but the sheriff is angered enough to not have doubts.
Another flashback sends us to the childhood of Joe Christmas. We see him around five years old, in the orphanage. Involuntarily he sees the orphanage dietician having sex with a man from the staff. Joe came to steal the toothpaste from the dietician’s room and thinks that now he will be punished for it, but she thinks that he will tell off her secret and insists on sending Joe to the separate orphanage for the black kids. We learn that actually Joe doesn’t look black at all! He had some traces of black blood, but he looks as any other white kid. It is the society that treats anyone with single drop of black blood as inferior. Joe is saved though: the man named McEachern adopts him unaware of his black heritage.
Joe grows up relatively happily. When he is seventeen he starts to secretly wander away and in the town, he meets a young waitress named Bobbie. Joe immediately falls in love with her, but Bobbie isn’t as serious about her feelings as Joe is. She is very interested in him in sexual sense though, so she meets with him oftenly. Once McEachern spots his stepson sneaking to the stable where Joe is hiding his fancy suit he uses to go to the dates. McEachern sees that Joe is picked up by the car and rides after it. He stops near the dance hall and see his stepson with Bobbie there. He rushes to Joe and starts to yelling at him, offending him, but Joe, enraged, hits him with a heavy chair. Mc. Eachern falls down, Bobbie runs away and Joe, frightened of what he has done, runs back home where he takes the money Mrs. McEachern kept for herself. Joe returns to Bobbie’s house, showing her the money and asking her to run away with him and marry him. But he sees Bobbie with another man she is ready to go to somewhere fancier than this town. The man, seeing Joe’s advances towards Bobbie beats him to half-death. Heartbroken and afraid that he killed his stepfather, Joe runs away to nowhere.
He can’t settle down for fifteen years, wandering through Chicago, Mexico and Detroit until he ends in Mississippi, working on the planing mill. At first, he tries to rob Joanna’s house, but she finds him and just feeds him willingly, seeing his miserable condition. She even allows him to live in one of her old buildings. Once, gratitude and sexual desire take over his common sense and he breaks into her house again and has sex with her. Ashamed of what he’s done he hides in his cabin until Joanna herself comes to him to comfort him and tell him the story of herself and her family.
Their relationship isn’t smooth, Joanna seems to be quite eccentric. Once she says that she is expecting a baby, but this appears to be a lie later. Still she cares about Joe trying to make him go and study in the school for the black people and become a lawyer, but Joe refuses. Not that he doesn’t want to study, but enrolling the school for blacks means admitting he’s black. When their relationship is almost over, Joanna asks Joe to pray with her, but he also refuses. Then she suggests they should commit suicide. Soon Joe kills her.
Joe goes into hiding and is pursued by the sheriff. Byron comes to Hightower and says that he offered Lena to live in the cabin that belonged to Christmas before. Meanwhile there are rumors that Joe is heading to Mottstown, a neighboring town to Jefferson. He is caught there without any resistance. Another man we don’t know yet named Uncle Doc Hines hears his name and rushes to the sheriff, screaming that Joe should be killed on the spot. When he comes back to his wife, Mrs. Hines bitterly asks him why he is so cruel to Milly’s baby. It turns out that Joe is the son of Hines’ deceased daughter. Uncle Doc and his wife head to Jefferson to see the trial.
When they come to Jefferson they meet with Hightower where they tell the history of real Joe’s origin. Their daughter Milly became impregnated by the black man from the traveling circus. Hines, avenging his daughter’s honor, killed Joe’s father, but Milly died later while giving birth to Joe. Without asking permission of Mrs. Hines, Uncle Doc took the baby and abandoned him near the orphanage. Still, Hines secretly watched the boy, not trying to contact him though. All that time Mrs. Hines thought he was dead. After hearing the story Byron asks Hightower to say that Joe was with him during the night of the murder - this evidence can’t be checked and will give Joe the chance to avoid the execution. Hightower refuses despite all the pleas.
Later Byron calls Hightower to Lena who goes into labor. The Hines family come with him. The former priest helps her to give birth to a healthy baby boy. Before he leaves, Lena tells him that Byron made a proposal to her, but she refused because she still loves Lucas. She also tells Hightower that Byron has abandoned his mill and went to the court to attend the trial. In the meanwhile Byron asks the sheriff to bring Brown to the cabin so that Lucas can see Lena and his son. Lucas is shocked and tries to make some excuses, like he is still searching for a job, he has powerful enemies to hide from and he will marry Lena as soon as the conditions are appropriate. But then he just runs away again through the window of the cabin. Byron is the only one to track him and call him out because of his actions. Lucas is ready to leave Jefferson by train. Byron chases him, and a fight starts. Byron is cruelly beaten and Lucas leaves. When Byron returns back, a man passing by says him that the trial is over and Joe is killed.
It appears that he wasn’t executed. The sheriff escorted him through the town, but Joe managed to escape and run away again. Percy Grimm, a young leader of self-proclaimed militia, pursued him and saw that Joe is running to Hightower’s home. We learn that Mrs. Hines came to Joe at night before the trial and said that Hightower would possibly help. Despite at the last moment Hightower changes his mind and says to Percy that Joe was with him at the night of the murder, the young man is too excited with the pursuit. He shoots Joe several times and then castrates him, still alive, with butcher knife.
The novel ends with Lena in her quest for Lucas. Byron decides to go with her and care about her and the baby. He still loves her and wants to marry her, but Lena is obsessed with Lucas.