The main theme of the novel is the contrast between Tom Jones's good nature, flawed but eventually corrected by his love for virtuous Sophia Western, and his half-brother Blifil's hypocrisy. Secondary themes include several other examples of virtue (especially that of Squire Allworthy), hypocrisy (especially that of Thwackum) and just villainy (for example Mrs. Western, Ensign Northerton), sometimes tempered by repentance (for instance Square, Mrs. Waters née Jones).
Both introductory chapters to each book and interspersed commentary introduce a long line of further themes. For instance, introductory chapters dwell extensively on bad writers and critics, quite unrelated to the plot but apologetic to the author and the novel itself; and authorial commentary on several characters shows strong opposition to Methodism, calling it fanatical, heretical, and implying association of hypocrites, such as the younger Blifil, with it.
The novel takes place against the historical backdrop of the Forty-Five. Characters take different sides in the rebellion, which was an attempt to restore Roman Catholicism as the established religion of England and to undo the Glorious Revolution. At one point Sophia Western is even mistaken for Jenny Cameron, the supposed lover of Bonnie Prince Charlie. Good-natured characters are often modestly loyalist and Anglican, even Hanoverian, while ill-natured characters (Mrs. Western) or only mistaken ones (Partridge) can be Jacobites or (like Squire Western) just anti-Hanoverians.