Based on the analysis of the characteristics of the supply chain system of complex products in cluster, this paper proposes to study the collaboration of supply chain system in cluster with the simulation technology. Under the condition of keeping the higher level of quick response, the key influence factors to the collaboration of supply chain system are found through the analysis of run results of simulation model. Some improving strategies are suggested according to the results. Contrasted front and back emulation results, the tactics are proven not only can effective reduced operation cost of supply chain, but also can improve the entirety operation efficiency of the supply chain system.