Abstract:Molecular Compatibility theory was put forward to provide theoretical guidance for modern Chinese medicine(molecular Chinese medicine).They were expounded to the background, scientific connotation, necessity,features of Molecular Compatibility theory and characteristics of modern Chinese medicine. Molecular compatibility theory had three features.①It reflected the concept of organic combination of Chinese and western medicine.②Systematic thinking combined with analysis reduction method organically.③The overall concept of TCM theory was adhered to;Characteristics of modern Chinese medicine by molecular compatibility theory was three.①They were clear of the chemical structure, molecular formula, molecular weight of all ingredients in prescription. ②The principle of dunchenzuoshi was followed. ③It had clear mechanism, definite effect, advanced dosage forms, stable quality control. ④ Multichannel, multi-evel and multi-channel network pharmacological effects were produced in sick body.⑤Efficacy was obvious and side effects were small for complexity, systemic diseases.The key to modernization of TCM was the modernization of TCM theory.Molecular compatibility theory, was the inevitable outcome of the development of The Times, which would promote the prosperity of Chinese medicine.