The central theme of Tom Jones centers on the concepts of virtue and vice. The story primarily highlights the virtue of prudence, while underscoring the vices of hypocrisy and vanity.

Prudence, a longstanding cardinal virtue in Western culture, involves foresight, assessing potential consequences of one's actions, and behaving accordingly. Tom's repeated misfortunes in the narrative result from his lack of prudence. Despite possessing virtues such as kindness, a generous heart, bravery, loyalty, and forgiveness, Tom's imprudence allows his adversaries to exploit him and nearly results in losing his beloved Sophia forever.

Tom's imprudence is frequently apparent in his dealings with women. Even though he loves Sophia, he continually engages in affairs with inappropriate partners. This behavior persists despite knowing it hurts Sophia and undermines his genuine wish to be with her.

Captain Blifil and his son, Master Blifil, serve as the main examples of hypocrisy and vanity, but they are not alone in this. Characters like Bridget Allworthy, Squire and Mrs. Western, the tutors Thwackum and Square, Black George, Lady Bellaston, Mr. Fitzpatrick, Lord Fellamar, and others also embody these vices in various ways. They resort to deceit, outright lies, betrayal, and slander to achieve their ambitions of wealth and social status. By illustrating these vices in numerous characters, Fielding suggests that such behavior is prevalent in the society he portrays, making it the norm rather than the outlier.

Fielding also examines the relative severity of different vices. His protagonist is far from perfect. Tom is openly promiscuous and often lets his desire for enjoyment lead him astray, even breaking the law, as demonstrated when he persuades Black George to join him in poaching on a neighbor's land. Throughout the novel, Squire Allworthy often expresses concern over Tom's actions and advises him on the importance of prudence and morality. However, until the story concludes, Tom frequently disregards this advice and falls back into his old patterns.

Despite being fully aware of Tom's shortcomings, Allworthy ultimately determines that Tom is fundamentally good, while Blifil is irredeemably bad. The overt and public vices Tom displays—which society often condemns most severely—are actually less serious than the hidden vices of vanity, hypocrisy, selfishness, and greed that characterize Blifil.

Allworthy's belief that Tom's shortcomings are less significant than Blifil's indicates that Tom has the potential for redemption, whereas Blifil does not. By the end of the novel, Tom is indeed redeemed. He acknowledges his mistakes, changes his behavior, and as a result, his "sins" are forgiven. He inherits Allworthy's wealth and wins the affection of both Allworthy and Sophia. In contrast, Blifil is cast out from the family.

The idea that Fielding is communicating a deeper message about redemption is reinforced by Allworthy's depiction as a God-like figure. He acts as a fatherly presence to both Tom and Blifil. Moreover, in his role as a magistrate, he is tasked with judging others and their faults. Throughout the story, he exercises this authority with kindness and restraint. He extends mercy to the powerless, such as Jenny Jones, and offers forgiveness to those who show remorse. It is reasonable to conclude that through the characters of Allworthy, Tom, and Blifil, Fielding suggests that people who are inherently good will be forgiven for typical human failings if they are willing to learn from their mistakes.