"Treatment based on diseases identification and formulas corresponding to diseases" is one of important therapy modes of Chinese medicine. Although it originates from Huangdi Neijing, it is seldom systematically discussed. Modern Chinese medicine (CM) now faces diseases mostly with comparatively confirmed Western medical diagnoses. Most of them have specific pathophysiological changes. How to interpret these specific pathophysiological changes, play CM's advantages, and improve clinical efficacies has become an inevitable problem for modern CM in clinic. Authors expounded historic development and clinical application of "formulas corresponding to diseases", and its difference from "formulas corresponding to syndromes", put forward that we should combine "formulas corresponding to diseases" and "formulas corresponding to syndromes" in CM clinics. We should focus on the disease and summarize treatment rules, thereby improving targeted CM formulas.