Yaodi Yuzhe (AD.1611-1671, named Fang Yizhi before his renunciation of mundane life) has long been known as the pioneer of textual research and natural history in Ming Dynasty; or has been considered to be the forerunner of Chinese modern science. Recently, Yaodi has also been considered to be the significant figure of advocating the syncretization of Confucianism, Buddhism and Taoism in the late Ming Dynasty. However, the status of Yaodi’s being the eminent monk of Caodong School in late Ming and his thoughts of Ch’an Buddhism have not yet been fully discussed. This article starts with discussing the “Action Orientation” of Yaodi and hopes to investigate the inner mind journey of Yaodi. From being the filial piety and the loyal ministers to Ch’an monk, he then enters the Qingyuan Mountains to rejuvenate the Cao Dong Zong, and finally he passed away with Samadhi in Huangkong Tan. Meanwhile, based on newly published Dong Hui Lu and Qingyuan Yuzhe Zhi Chanshi Yulu, and making use of other important original materials concerning the Ch’an Buddhism thought of Yaodi, such as Dong Xi Jun, Qingyuan Zhilue, Yaodi Paozhuang and Yi Yu, this article explores the thought of Yaodi’s Benfen, Ch’an and its introspection on “Crazy Ch’an” in late Ming dynasty, the thought of Yaodi’s literal Ch’an under the popular trend of consistency of Ch’an and Teaching in late Ming dynasty, Yaodi’s syncretization of Confucianism, and Buddhism thought under the background of communion of China and Indian thought. Through the above exploration and analysis, this article emphasizes Yaodi’s unique status in the spiritual transformation of Ch’an Buddhism in late Ming dynasty.