Under the background of China is actively expanding imports, this paper investigates the effects of quality of imported intermediate inputs on enterprise innovation performance using patent data of enterprises. The empirical results show that: (1) Quality of imported intermediate inputs will improve the quality of enterprise’s patent application. It can significantly promote invention applications, reduce design applications, and has no effect on utility model applications. (2) According to the mechanism analysis, quality of imported intermediate inputs will promote enterprise’s innovation performance by expanding market size, improving productivity and human capital, but it does not affect enterprise’s innovation performance by intensifying financial constraints. (3) Further analysis shows that, when intellectual property protection is improved, the promotion effect of quality of imported intermediate inputs on innovation performance of enterprises in patent intensive industries will be weakened. Therefore, China should attach great importance to the promotion effect of quality of imported intermediate inputs on innovation performance, and strengthen intellectual property protection strategically.