By adopting Propensity Score Matching Method and establishing Propensity Score Matching model, this paper conducts an empirical analysis of the incentive effect of financial subsidies to the investment in innovation based on 66 new energy automobile companies listed during 2012 and 2017.The results reveal as follows: financial subsidies can effectively promote new energy automobile industry to carry out innovation activities, and it has a positive effect on both capital and staff. Therefore, it is suggested that overall subsidy intensity of new energy automobile industry be increased, a R&D subsidy regulatory subsidy mechanism established, and the system of intellectual property rights protection improved , so that financial subsidies can play a better role of motivation on new energy automobile industry.