ZHOU Shenzhai was a famous doctor in the Ming Dynasty, who attached great importance to regulating spleen and stomach. What’s more, he made good use of Baoyuan Decoction (保元汤) to treat internal injuries and miscellaneous diseases. He was so proficient in pulse diagnosis and using traditional Chinese medicine. ZHOU Shenzhai’s students recorded his clinical experience and compiled to a book named The Medical Book of ZHOU Shenzhai, in which Baoyuan Decoction was included. This article discussed this decoction about its historical evolution, component, clinical application and modification from the perspective of ZHOU Shenzhai using Baoyuan Decoction based different diseases and complex syndromes. He thought highly of the therapy of regulating spleen and benefiting vital Qi, and then introducing the therapeutics above flexibly in order to recover the normal physiological Qi of spleen, lung and stomach. This article provided a brand new thought of clinical application of Baoyuan Decoction, which would make a profound influence on inheriting and developing traditional Chinese medicine.