Using the Quasi-Natural Experiment of establishing administrative approval center and combined with Chinese micro enterprise data, this paper studies the impacts of administrative approval system reform on enterprise innovation with the difference-in-differences and triple difference methods. We find that administrative approval center significantly improved the level of enterprise innovation and after a series of robustness tests, the conclusion remains valid. However, there are differences in policy effect between the type of patents and firms. Specially, utility model and appearance design patent, domestic-funded enterprises, firms close to the international technological frontier and firms in low external financial dependence and non-patented intensive industries benefitted more from the institutional reform. Finally, from the perspective of influence mechanism, Administrative Approval Center obviously reduced institutional transaction cost and fostered R＆D and technological innovation for enterprises on the one hand. Yet on the other hand, the improvement of administrative approval efficiency promoted enterprises entering and squeezed the living space of incumbent enterprises, which discouraged innovation.