Abstract: From the view of input and output, this paper makes an empirical research to explain elastic relationships between government S&T funding for different innovation subjects and regional R&D output based on panel data from China, focusing on the performance research of funds to different recipients, and explores it under different level of government support in research systems. The results indicate that the government S&T funding for technological innovation subjects has positive effects on R&D output significantly and the elasticity of them presents diversely. Besides, under the different intensity of government support, elasticity coefficients of scientific research institution, university and enterprise successively get lower, higher and almost unchanged. This study provides critical suggestions to optimize government S&T funding in the configuration among innovation subjects to contribute to R&D output.