Based on the data of China’s A-share listed strategic emerging industry companies from 2011 to 2019, this paper discusses the impact of economic policy uncertainty on R&D innovation. The research shows that the uncertainty of economic policy inhibits the R&D innovation of companies in strategic emerging industries; In the analysis of heterogeneity, it is found that under different property rights and asset scales, the uncertainty of economic policy can inhibit the R&D innovation of companies in strategic emerging industries, especially for non-state-owned or small-scale companies. Based on the research conclusion, this paper suggests that the government should continue to build a fully competitive, fair, transparent and open business system, and strategic emerging industry companies should take measures to improve corporate governance quality to alleviate the impact of economic policy uncertainty.