Based on the panel data of GEM listed enterprises from 2014 to 2019, an inquiry has been made into the relationship between accounting conservatism and innovation performance, followed by an introduction of financial subsidies for an empirical test of whether they play a regulatory role in the relationship between them. On this basis, a further investigation has been made of the impact of the nature of ownership on their relationship. The empirical regression results show that the higher the accounting conservatism is, the lower the enterprise innovation performance will be, with a significant negative correlation between them. The acquisition of financial subsidies can effectively alleviate the inhibitory effect of accounting conservatism on innovation performance, thus helping enterprises enhance innovation performance. After a distinction of the nature of property rights, accounting conservatism has a more significant inhibiting effect on innovation performance in non-state-owned enterprises than in state-owned enterprises.