His 2002 dissertation, The Terrible, Horrible, No Good, Very Bad Truth About Morality and What to Do About It, argues against moral-realist language and in defense of non-realist utilitarianism as a better framework for resolving disagreements.

In particular, Greene argues that the "central tension" in ethics between deontology (rights- or duty-based moral theories) and consequentialism (outcome-based theories) reflects the competing influences of these two types of processes:Characteristically deontological judgments are preferentially supposed by automatic emotional responses, while characteristically consequentialist judgments are preferentially supported by conscious reasoning and allied processes of cognitive control.

[9] They also found that for the dilemmas involving "personal" moral questions, those who did make the intuitively unappealing choice had longer reaction times than those who made the more emotionally pleasant decision.

Greene's 2008 article "The Secret Joke of Kant's Soul"[15] argues that Kantian/deontological ethics tends to be driven by emotional responses and is best understood as rationalization rather than rationalism—an attempt to justify intuitive moral judgments post-hoc, although the author states that his argument is speculative and will not be conclusive.

[16][17][18][19][20][21] Drawing on dual-process theory, as well as evolutionary psychology and other neuroscience work, Greene's book Moral Tribes (2013) explores how our ethical intuitions play out in the modern world.

[22] Greene posits that humans have an instinctive, automatic tendency to cooperate with others in their social group on tragedy of the commons scenarios ("me versus us").

In response, Greene proposes a "metamorality" based on a "common currency" that all humans can agree upon and suggests that utilitarianism—or as he calls it, "deep pragmatism"—is up to the task.

Greene's metamorality of deep pragmatism has recently been criticized by Steven Kraaijeveld and Hanno Sauer for being based on conflicting arguments about moral truth.