The Slave Dancer centers on a young boy's journey toward understanding himself. At just thirteen, Jessie Bollier finds himself entangled in the schemes of a corrupt society. Separated from his family and friends, he must define his identity through his actions while enduring psychological, moral, and physical isolation. Jessie, the ship's sole musician, is also the only white person who sees the slaves as fellow human beings. To his dismay, he starts to adopt some of the older crew members' attitudes as the journey unfolds. Although he cannot physically oppose the slavers, he resists them morally and intellectually, which enables him to survive and grow.

The ship's crew and officers are a motley group of characters. They range in moral character from the straightforward yet honest sailor, Clay Purvis, to the scheming and deceitful Benjamin Stout, to the cowardly and brutal mate Nicholas Spark, and finally to the erratic, cruel, and selfish Captain Cawthorne. The other adult sailors are less distinctly portrayed, their personalities largely shaped by the moral decay resulting from their work on the slave ship.

Ras, the young slave who escapes the shipwreck alongside Jessie, is the only slave in the story who is named. Fox does not delve into the personalities of the other slaves; they only stand out as individuals when they fall victim to specific acts of cruelty. Daniel, the elderly black man who aids Jessie and Ras after the shipwreck, starkly contrasts with the crew and officers of The Moonlight. He does not judge based on race; instead, he sees two young men in need and offers them water, food, and shelter. Daniel, Ras, and Jessie's mother and sister are minor characters who reflect Jessie's disregard for race and detestation of slavery.

A few secondary themes revolve around Jessie's primary struggle with society. Among the topics Fox examines are battles with conscience, the transition into adulthood, poor communication with older generations, emotional suppression, alienation, and perhaps most poignantly, the complexity of justice in a world where a slave ship is destroyed, yet nearly all the slaves perish.