Abstract: The effective synergy among government, entrepreneurial carrier and incubated enterprises has an important impact on the development of enterprises, government performance and regional innovation. Based on the perspective of cross-organization synergy, this paper discusses the synergy among government, entrepreneurial carrier and incubated enterprises, and empirically tests their synergistic impacts on the cooperation performance of incubation system, and the moderating effect of cooperation intention on the relationship between synergy and cooperation performance. The results show that the degree of resource sharing，the consistency of interest orientation and the degree of institutional synergy will affect the cooperation performance among these three. And cooperation intention can respectively promote the relationship between resource synergy, interest synergy, institutional synergy and cooperation performance. This paper provides empirical evidence and practical reference for the innovation and sustainable growth of start-up enterprises.