Marriage is the central issue in this novel. This is true in the practical aspects of marriage as well as the ideological elements of the institution.
Jude's marriage to Sue is the most significant one in the novel, but far from the only one. Jude also marries Arabella and Sue also marries Phillotson. Arabella also has a second marriage.
Each of these unions is examined in terms of its honesty and in terms of its balance. Conversations abound regarding the logic of a permanent bond formed between two humans fated to change their minds about their preferences.
Jude's marriage to Arabella, like Sue's marriage to Phillotson, grows out of obligation and deceit, not love. Yet the legal bond endures long after the emotional bond is broken. This lamentable fact also is discussed at length.
The bitterness of "false" marriage marks both Sue and Jude.
Sue’s marriage to Phillotson has led her to despise the institution, much as Jude’s problems with Arabella Donn had caused him to be fearful.
The practical and legal difficulties that grew from their failed marriages are clearly drawn in the novel. The ideological difficulties of marriage are explored throughout the novel but find fullest expression in the extended pseudo-betrothal between Jude and Sue.
As Jude and Sue are freed to marry one another after each getting divorced from their first marriages, they postpone doing so.
Several debates take place that articulate varying challenges to the legal structure of marriage, the moral (and demoralizing) effects of marriage on individuals, and the natural resistance of free spirited people to such a permanent institution.
Marriage is defined by rules. Society sees marriage, in this novel, as a set thing. To play with the rules of marriage is to endanger the society. This notion is demonstrated when Phillotson is fired from his teaching position after the town discovers that he permitted Sue to leave him so that she could live with her lover.
Phillotson gives his consent to her departure; when his superiors at the school discover the arrangement, he is relieved of his position.
The town, as a representative of society, was not even slightly interested in allowing a breech of the well-understood protocol surrounding marriage. To challenge the institution of marriage is to challenge the moral authority of society at large. Acting unconventionally leads to ostracism, as we see with Phillotson and later with Jude and Sue as they are run out of town.
Marriage, in light of these arguments, can be seen to symbolize social rules generally, which often stand in opposition to the will of the individual.