In 1996, Whitaker married fellow actress Keisha Nash, whom he met on the set of Blown Away. The Whitakers have four children: two daughters together (Sonnet and True), his son (Ocean) from a previous relationship, and her daughter (Autumn) from a previous relationship. Whitaker, who is a vegetarian, has recorded a public service announcement with his daughter, True, promoting vegetarianism on behalf of People for the Ethical Treatment of Animals (PETA). In politics, Whitaker has supported and spoke on behalf of Senator Barack Obama. Whitaker also studies yoga and has a black belt in karate.

Whitaker's left eye ptosis has been called "intriguing" by some critics and "gives him a sleepy, contemplative look." Whitaker has explained that the condition is hereditary and that he has considered having surgery to correct it, not for cosmetic reasons but because it affects his vision.