Jude Fowley is 11-year-old boy who lives in the small village of Marygreen. He is an orphan, so Jude is raised by his aunt. He dreams to enroll the university and get the career in science. Jude is encouraged with success of his schoolmaster named Richard Phillotson, who moved to the bigger town of Christminster planning to become a scholar. But Jude’s aunt has a much more pragmatic worldview, so she insist that Jude becomes a stonemason. Still, the boy tries to educate himself, learning Ancient Greek and Latin and hoping that someone he will go to Christminster.
Nevertheless, all his plans are disrupted by the young woman named Arabella. Arabella is rude but witty and beautiful. Jude likes her, but isn’t sure about his intentions - the dream about university has the first place in his soul. But Arabella has another plans: she tricks Jude into sleeping with her and then claims she is pregnant. Jude has no option. Either he is publicly disgraced or he marries Arabella and lets go the dream about scholar career. But right after marriage she tells Jude that she was wrong about pregnancy, so actually they are not going to have a baby now.
Jude feels wronged, and Arabella’s personality is still rough. The marriage gets worse and worse and finally they decide to break up. Arabella moves to Australia with her family. At first, Jude feels very enthusiastic, he can now return to his dreams about Christminster and university. But when he does manage to move to the town he faces the cruel reality: it is very hard for the poor, self-taught orphan to enroll the university. Anyway, Jude doesn’t want to give up. He finds a stonemason job - his skills are fine even for such a place as Christminster - and continues self-education hoping to try again next year.
Soon Jude meets his cousin, Sue Bridehead. It is the first time he meets her in person, but Sue’s portrait always stood in his aunt’s house and he really liked the mysterious girl. At first, Jude just follows her without being noticed - as the girl from the portrait, but then they finally talk and befriend each other. He tries to stay focused on study, but after the troubled marriage with Arabella he is enchanted by Sue’s persona and appearance. Sue is going to leave Christminster soon, so in anattempt to make her stay Jude finds his schoolmaster Phillotson and asks him to take Sue as his secretary. Sue agrees and everything seems to go fine, their relationship even looks like improving.
But soon Jude learns that Sue and Phillotson become engaged. Sue really feels a lot towards Jude but decides to marry Phillotson anyway. She is unhappy in the marriage, though - she just can’t stand her husband and he also treats her not as she deserves. Their marriage also fails miserable as Jude’s and Arabella’s before and at last rebellious Sue leaves her husband and goes to live with Jude.
Finally, the situation is really improving. Both of them divorce (Arabella comes to say that she married another eccentric man in Australia, so Jude can freely end their relationship), but Sue isn’t willing to marry again. She doesn’t want neither sex nor another marriage, but Jude is ready to wait until she is okay. Later they work out this issue and live together as a couple, raising two children.
But then Arabella shows up again. She tells Jude that she left him pregnant and gave birth to his son eight months later, in Australia. Now she wants to send the boy to his biological father. Amazingly, Jude buys for this trick one more time and feels obliged to take quiet, gloomy and reserved boy into his family.
The society doesn’t tolerate such kind of relationship, people see only a love affair and children born out of wedlock. Due to a huge scandal Phillotson has to quit teaching, his career is ruined. So is the career of Jude himself - his employer fires him immediately after knowing about what has happened. The family has to move from town to town in search for a job. It is also a trouble for Jude and Sue to rent a house or even a room - people don’t want to see such a couple in their houses.
They have troubles with their elder son (of Jude and Arabella), also called Jude. He is even nicknamed as Little Father Time for his gloomy worldview. He quickly gets used to Sue even calling her his mother, but his manner of speaking and behaviour seem to belong to much older person than he is and a disillusioned one. There is nothing childish in him and nothing can make him happy.
The family has less and less money for living. Finally, after Jude’s illness, they decide to return to Christminster. Observing their troubles, Jude Jr. becomes more and more serious and determined. The last straw is his father who needs to rent a separate room, because it’s too hard to find the place for so many children with such a reputation. One day Sue goes out for a while to have dinner together with Jude and upon returning finds that her elder son hanged his siblings and himself, leaving a note that there were too many of them. Sue, pregnant with her third child, has a miscarriage because of shock.
Sue is devastated by loss of all her children. She tries to find the meaning of life in religion but comes to the conclusion that what happened was God’s punishment and she had to stay with her husband. She doesn’t want to return to Phillotson, but feels obliged to. Arabella (showing in Christminster again) pushes her towards him and Sue ends up marrying Phillotson again.
Arabella catches Jude at his lowest and encourages him to drink more and more, finally tricking him to marry her again. Jude seems to not care anymore, he is a heavy drinker at the time and gets more and more ill. Feeling that his time is coming he makes the last desperate attempt to find Sue. They talk and express their still mutual feelings to each other ending with a kiss. But Sue, afraid of God’s wrath, refuses to run with him. Jude returns home and dies soon after. Arabella doesn’t seem to mourn him very much, starting to look for another husband almost immediately. Sue lives the rest of her miserable life with Phillotson.