Developments in neurobiology are providing new insights into the biological and physical features of human thinking, and brain-activation imaging methods such as functional magnetic resonance imaging have become the most dominant research techniques to approach the biological part of thinking. With the aid of neurobiology, there also have been several studies on the biological processes of human moral thinking in moral psychology. For instance, some researchers have tried to discover patterns of brain activation when a person copes with moral dilemmas. In this paper, the authors suggest the level-structure of moral thinking from the most abstract level to the most biological-physical level and reductionism in the philosophy of science is introduced as a framework for analysis. Moreover, with the level-based structural approach and framework of reductionism, this paper tries to discover the practical value of our model for moral development and education.