Scholars usually regard the late Ming dynasty (1368-9644) a reformation period in thoughts, and claim the Ming neo-Confucianism being the counteraction to Song neo-Confucianism, the expansion of ego-consciousness in literature and arts being the reaction to Confucianism, and the highlighting of sexual life being the reaction to the emphasis in Confucian preaching, etc.. This kind of fragmental and diverged interpretation of history and individual consciousness, in my opinion, are the projection of modern concepts instead of the fact in the late Ming. The trend of thoughts then should not be divergence but harmonization. Not only the harmonization among Confucianism, Taosim and Buddhism were proposed, there was even a tendency of harmonization inside each religion. This article aims to elaborate this point with the example of Ou Yi Zhi Xu, an eminent Buddhist monk then. When discussing Buddhism in the late Ming, scholar also tends to classify it as Zen as a whole, or taking Zen as the background to study Buddhism and its relations with Confucianism, and are ignorant about the fact that the situation of the late Ming Buddhism was also complicated. In fact there were Tiantai, Pure Land, Vinaya and other Buddhist schools in the late Ming. Each school had their own prominent masters, most of whom preferred their study in a synthetic way. Master Zhi Xu was an important example who paid attention to most of the aforesaid Buddhist schools. In addition, he linked the Buddhist Tripitaka to Confucianism and even made his exegesis to the Book of Changes. It is worthwhile to study how he synthesized the various kinds of philosophy. Nevertheless, the topics stated above are not studies in this article. Though the study of late Ming Buddhism is rare, there have been some papers which mentioned Zhi Xu’s contributions to Tian Tai, Pure Land and Vinaya schools. Therefore the focus of this article is on his study in Vijnapti-vadin. Thr Ci En sect of Vijnapti-vadin almost came into extinction after Kui Ji and Yuan Ce. It revived in the late Ming, and Master Zhi Xu was one of its masters. However, Zhi Xu was not only a follower of the old philosophy. A higher understanding of truth was made through his emphasis on both Nature and Appearance, and the concept of "Observing the Mind" as well. This article investigated its theory structure and background of establishment, in order to provide a reference to the historians.