By taking complex system idea, based on HLA(High Level Architecture) standard simulation, by using multi-Agent simulation research method for complex system, this paper designs multi-Agent simulation system structure for traditional Chinese medicine, by taking federate Agent structure of stasis syndrome as an example, proposes basic intelligent simulation agent basis—Traditional Chinese Medicine Intelligent Model, based on differentiation of eight principles, theory of differentiation of Zang and Fu, and clinic experience of each school of traditional Chinese medicine, by absorbing intelligent Agent clinic information of four diagnosis methods and micro-bio-chemical gene information, by using intelligent model and computation, designs federate Agent for syndrome mechanism, compatibility of medicines in a prescription, and combination of all methods, meanwhile, by using communication Agent and RTI(Run Time Infrastructure), sets up system control structure, further puts forward the complexity research on the coordinated mechanism and intelligence function of this simulation system, and finally tests the correctness of this system by comparing the diagnosis results between experts and simulation system under different samples.