Yongle Emperor (Chengzu of the Ming Dynasty) decreed to compile Encyclopaedia of the Four Books (Sishu daquan). Under the imperial authority, scholars changed their way of pursuing studies. The Four Books, therefore, transcended the Five Classics and became the core of the Confucian Philosophy. In order to analyze the contents and citation in the Encyclopaedia of the Four Books, I inspect the process of compiling as well as verify the texts, and then generalize three conclusions. First of all, the system of Zhu Xi, constructed by Zhu’s disciples, is full of the compilation and confirmation of Zhu’s interpretation. Second, divergent statements from academicians of Shuang-Fong and Bei-Shan Schools. Third, the scholars of Xin-An school, whose main purpose is to revert to Zhu Xi’s original way of doing research, which is integration and analysis. From inheritance to divergence, and then from divergence to integration, the three systems interacted with each other. Encyclopaedia of the Four Books annotates the achievement of the Four Books through Xin-An School, who inherited Yuan scholars’ ideas, on one hand. This work reflects the arguments among Xin-An academicians, Shuang-Fong school, and Bei-Shan school, on the other hand. Effort (gong-fu) and gradation (jing-jie) finally became the focus of attention. Hence, scholars think of these two issues over and over again and want to make a final version. To Ming scholars, interpretation of mind and principle in the Encyclopaedia of the Four Books is the foundation of understanding Zhu’s study. Their discussions give posterity many fresh thinking ways and change the academic trend. Before Ming Dynasty, scholars did not deeply research on the interpretation of mind and principle. And this is the reason why Zhu’s study declined. Many Yuan scholars’ works were lost and the clues were vague. In order to give a clear explanation, I will collect and compare the texts again.