This paper deals with the social system from the point of system thinking consisting the fundamental construct of system dynamics. The Bertalanffy′s general system theory, having been criticized because of its ambiguity, and the complex science theory, emerging system theory, are integrated by using the system thinking which is characterized with three concepts, ′feedback thinking′, ′dynamic thinking′, ′operational thinking′. In the integration, system thinking suggests the dynamic pattern of the social system have not only an equilibrium status but also complex status. The science of complexity gives an implication to system dynamics the important of the uncertainty and complexity if we interpret the social system as an open system. To show more concrete description, I simulate the cooperation model based on the iterated prisoner dilemma. The simulation results show the diverse patterns of cooperation and betrayal. Especially the sensitivity of initial payoff will cause the chaotic strategic landscapes as the game gose on. These results mean that we should not give the hasty prescription to control social system artificially. Because social system retains the self-organizing force in itself.