Themes that permeate the narrative in The Indian in the Cupboard are prejudice and the responsibility that comes with power over people.
The theme of prejudice comes into play when Little Bear is first introduced to Boone and the two are immediately mistrustful of one another. Boone thinks of Little Bear as a bloodthirsty savage, and Little Bear thinks of Boone as ignorant and presumptuous. When the two are introduced to western television, this mistrust erupts into almost mortal violence. In the aftermath, however, the two are able to reconcile their differences and become closer than brothers.
The theme of the responsibility of power also plays a role. When Little Bear is first brought to life by Omri, he thinks that the latter is a god. While this turns out to not be true, the amount of power that Omri has over Little Bear is all but omnipotent. He's not a god, but he may as well be. After many missteps, Omri realizes that Little Bear is a living being worth of respect and not a toy to be played with, despite the fact that Omri has the power to do so.