With the development of Small and Medium-sized Enterprises (SMEs), their mutual cooperation is playing a significant role in promoting China’s economy. In this paper, we build an evolutionary game theory model of SMEs’ cooperation capturing the evolution of SMEs’ mutual trust dynamic process. It is found that the direction of the system’s evolution depends not only on the game payoff matrix but also on the initial state of the system. Other key factors influencing the SMEs cooperation are monitoring frequency, punishment intensity and counterfeit cost. The conditions for the enterprises cooperation are found. This research helps us understanding how to guide enterprises to achieve win-win business.