Complex system is a new challenge to our era．We conclude that complex system research must be cross-discipline research．To conquer the complexity of complex system，we should synthesize theories from multi disciplines，qualitative and quantitative：methods，thinking of mankind and computing of computer． First the main areas and methods of complex system research are summarized．Guided by metasynthesis theory，we studied the methOds for complex system research，restated Traditional Chinese Medicine（TCM） theory in new view，developed an evolutionary computing model in practice． For methodology，the Open Complex Giant System theory，work of Santa Fe Institute，Cybernetics method and TCM theOry are discussed in depth·After study on Reductionism，Holism，bottom-up，top-down， modeling approach and TCM method，we synthesized a Function-Relation method to study the global structure，function and relations in complex system． TCM is a unique accomplishment on complex system in China．We tried to answer an essential question by comparing TCM philosophy and Scientific methodology：How can TCM be effective in practice and be different from western science at the same time?The main framework and ideas of TCM are restated in systematic view，especially the holism idea， the man．earth relation idea，Yin-Yang and Five Phrases model． Evolutionary Computing model is a major approach for complex system research．We observed that most difference between Genetic Algorithms and nature fall into the same system：diploidy structure， dominance mechanism，meiosis and the dynamic environment．The former GA research only studied part of this complex integrated system，didn't realize the structure and its operation come from coevolution and fit each other．A new evolutionary computing model was designed to implement this，tested on a Hamiltonian Cycle Problem．The experiment developed our understandings on algorithm，model and biology．
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