The moral ontology of Neo-Confucianism expresses much more concern for virtue and sanctification than the whys and wherefores of everything in the universe. It focuses on how morality is formed and the reason and basis of morality; it endows morality with primacy and absoluteness through the construction of moral ontology. Starting from the mysterious and dominant “Tian”, it draws on the absolute dominant force of Heaven to emphasize the absolute authority of morality. Zhang Zai took the intrinsic nature as the ontology and turned the authority of morality from external restraints to human voluntariness and self-consciousness. Cheng Hao, Cheng Yi and Zhu Xi, with the idea that “all things in the world are but one law”, ascended the ought-to-be code of conduct and seniority in human relationships to the inevitability of the existence of the universe. The external coercive force of the “li” could easily deprive the subject of the internal motivation to practice morality; in the course to “unity of xin and li”, the perceptual role of “mind” could easily dilute the sanctity of “li”. The philosophy of the xin criticized Cheng Hao, Cheng Yi and Zhu Xi for “parting xin and li into two” and proposed “the ontology of xin”. By cognizing the inevitability of the existence of the universe and the normality of the way of the world with “mind” and achieving their unity, the subjectivity of the human was taken to the extreme. But the individualization and emotionalization of mind would cause the risk of self-disintegration of moral ontology. The clarification of the way of generating moral ontology of Neo-Confucianism is beneficial to explain the thinking characteristics and theoretical predicament of the ontology of Neo-Confucianism, and to reveal its self-sublation and self-development in repeated interpretation and criticism.