What is the relationship between traditional Chinese medicine and history of Sino-Japanese War? Firstly, this study performed an overview of pharmaceutical industry during the Sino-Japanese War, and then probed into the complexity of several concepts, such as the overall domestically manufactured drugs, western medicine substitutes, and Chinese drugs. All in all, the war contributed to the development of planting and research of Chinese drugs. The pressure of war brought traditional Chinese herbal medicines to the spotlight of scientifically manufactured drugs. The investigation on the development history showed that the research of traditional Chinese herbal medicines was not performed based on the theories of traditional Chinese medicine, but the initiation of botanical and chemical R&D of traditional Chinese herbal medicines. To military medical units who urgently needed drugs, the so-called substitutes of domestically manufactured drugs under R&D were still “western medicines,” instead of traditional Chinese herbal medicines of traditional Chinese medicine. Besides, the importance was not attached to the medical principles behind traditional Chinese medicine at the time. Such R&D were still the implementation of post-westernization pharmaceutical concept. Moreover, particular stress was laid on the research and analysis of a single traditional Chinese herbal medicine. The entire effort required the attention of state-level units or funds. On the contrary, unfortunately, the pharmaceuticals and pharmaceutical research within the military medical system was terminated briefly in 1945. However, the overall research methods were continuously developed, which inspired the development of modern traditional Chinese medicine. A large amount of traditional Chinese herbal medicines were further planted and refined through botanical re-inspection and chemical laboratory analysis to create a variety of over-the-counter drugs. Although such drugs were used as “substitutes,” they also verified the “efficacy”of traditional Chinese herbal medicines, which undoubtedly was breakthrough and innovation.