Based on the panel data and threshold effect model of China"s strategic emerging industries from 2000 to 2015, this paper empirically examines the Relationship between Government R D Funding, institutional environment and innovation performance. The results show that the institutional environment has a significant positive moderating effect on the relationship between Government R D Funding and innovation performance. The industrial scale, export scale and capital input have positive effects on innovation performance, while the property right has negative effects. The effect of technology import is not significant. Compared with the central and western regions, the institutional environment in the eastern region is more favorable, and government R D subsidies have a more significant promoting effect on innovation performance. The institutional environment plays a regulatory role mainly through the relationship between the government and the market. Therefore, it is of great significance for the innovation and development of strategic emerging industries to fully understand the importance and urgency of regional institutional system construction and promote the effective integration of government R D subsidy policies and institutional environment construction at a higher level.