Modern epidemiology led to a comprehensive change in social concepts. As a result, the fear of bacteria became a psychological basis of social mobilization in modern countries. In China, the fear of bacteria and the fear of Western forces were ingeniously combined, thus becoming the emotional motivation for New Culture intellectuals who fervently criticized traditional Chinese medicine under the slogan of scientism. In the context of the debate between Chinese and Western medicine, this article focuses on the writings of infectious diseases in modern Chinese literature. By analyzing the texts and events related to Chen Dabei, Sun Fuyuan, Lu Xun, Ye Shengtao, Wang Luyan, and Xu Qinwen, this article reveals the interstice in modern Chinese literature created by the subtle tension between enlightenment and scientism, and also demonstrates the situation of traditional Chinese medicine in the modern period, in order to provide a new case for reflecting on modern Chinese literature from the perspective of traditional knowledge.