Tom displays a realistic combination of strengths and weaknesses. Living with a childless couple who do not seem to understand him, he develops an intense longing for companionship, which is fulfilled by Hatty, the girl he meets in the garden. Preoccupied with his own feelings, Tom is not always considerate of others, but he matures during the course of the story and develops greater sensitivity. Hatty is also a lonely child, orphaned and living with an aunt who is extremely unkind to her. Her friendship with Tom is important to her, and their disagreements, as in the scene where each accuses the other of being a ghost, are dramatic and convincing.
Hatty lives with three cousins—Hubert, James, and Edgar. Hubert, the oldest, has little importance in the story, but James is portrayed as gentle and understanding, while Edgar is mean minded and delights in getting Hatty into trouble. A better friend to Hatty than any of these boys is the gardener, Abel, a devoutly religious man who tries to protect her from harm.
Several adults appear in the story, including Tom's aunt and uncle and Hatty's aunt and uncle. Tom's Uncle Alan is a well-meaning man, but rather too rigid in his thinking to understand an imaginative youngster like Tom. Aunt Gwen, having no children of her own, smothers Tom with maternal affection although she does not really understand him. Hatty's aunt and uncle have taken her in out of necessity after her parents died. The aunt, in particular, is coldhearted and snobbish, the one real villain in the story. The landlady, the elderly Mrs. Bartholomew, takes on increasing significance as the plot unfolds. Her conversations with Tom are warm and genuine and contrast with the bumbling attempts of other adults to talk with youngsters.
Tom's Midnight Garden is thematically rich. The major themes are the nature of time, the patterns of growth and transformation, the relationship of past and present, and of youth and age. The most important theme is that of time, first introduced by a symbolic object—an old grandfather clock that strikes the hours with eccentric irregularity, occasionally even striking thirteen. Different conceptions of time are experienced and then discussed by the characters. Hatty shows Tom the message imprinted within the clock: "Time no Longer"—a phrase taken from a verse in Revelation. For Tom, time seems to stop when he is in the magical garden, but it races ahead for Hatty, who grows up while he stays the same. When Uncle Alan tries to explain the nature of time by drawing a diagram on a piece of paper, Tom realizes that his own conception is not nearly so mathematical. Tom's speculations on the nature of time grow more complex as the book progresses, and his perceptions, although imaginative, become more meaningful than his uncle's scientific explanations.
Closely related to the idea of time is the relationship between past and present and the inevitability of change. Where the lovely garden existed in the past, there is now but a strip of paving where dustbins are kept. The spacious home that once housed a single family has been converted into smaller flats that house many couples and families. What has not changed is the timeless nature of the young people's enjoyment of the garden.
"Don't be a fool! It's there, I tell you! The garden's there!"
Also related to the theme of time is the relationship of youth and age. Neither Tom nor Hatty achieves a good relationship with their respective aunts and uncles, and, to an extent, the adults in their world seem to lack understanding of youngsters. The notable exception is Hatty herself, grown old as Mrs. Bartholomew. In a touching conversation, she and Tom share their dream experiences and find that they have become close friends, in spite of their vast separation in age and years. When Tom bids her farewell, he hugs her, as his aunt notes, as if she were a girl. Pearce seems to suggest that age, as such, does not separate people, but attitudes do.