As a famous scholar of late Ming and early Qing Dynasties, Fang Yizhi's academic achievements have been highly praised. However, little was known about his advocation of confluence of Chinese and Western medicine. Through the author's study, it is evident that Fang Yizhi introduced new ideas on human anatomy and physiology spread by western missionaries. His records that "brain is responsible for memory", "brain governs movement and sensation" embodies the description of confluence of Chinese and Western medicine and is the earliest of its kind of his contemporaries. His summary of "zhiche", "tonji" on the art of Chinese and western knowledge is a conclusion in principle and universally accepted in the academic field. The so-called "superior-inferior-spring-autumn", "configuation-nature and Qihua" conception from main exponents of confluence school, Wang Xuequan, Tang Roagehuan, Zhuk Peiwen is derived from Fan's idea.