Altruistic punishment is very common in human life, which is an effective mechanism enforcing group cooperation and social norm. From perceiving the transgressions to administering costly punishment, potential punishing requires a series of cognitive and affective processes, including fairness judgment, reward processing, self-control, mentalizing, etc., and their underlying neurophysiological mechanisms. Cognitive neuroscience provides alternative perspective and paradigm for understanding human punishment behavior. Based on the latest findings, the neurophysiological mechanisms of altruistic punishment are reviewed and discussed in this article.