Abstract: As China's national strategy, civil-military integration is in the key period of transition from the primary stage to the deep integration stage. Civil-military integration innovation is an important means to promote the development of dual-use technology and realize industrial upgrading. However, whether the growth of government subsidies in different innovation activities of civil-military integration enterprises can promote the improvement of enterprise performance remains to be verified. Therefore, this paper study the relationship among government subsidies, innovation heterogeneity and enterprise performance of civil-military integration listed companies’ innovation activities. The results show that: (1) government subsidies have a significant positive impact on innovation input and innovation output of civil military integration enterprises. (2) The results show that government subsidies have a better supporting effect in research-oriented innovation activities, but not in development-oriented ones. (3) In terms of innovation input and output, state-owned enterprises are better than private enterprises, while in terms of enterprise performance, the opposite is true. (4) The transmission channels of government subsidies on enterprise performance from high to low are research innovation input, innovation output, and development innovation input. Therefore, it is significant to improve the effect of government subsidies through the reform of system and mechanism, breaking down the barriers of enterprise nature and improving the conversion rate of achievements, which is very important to promote the innovative development of civil-military integration in China.