Although policy support for emerging industries has become an important choice for the world's major economies, the deviation between policy objectives and the status quo of industrial development indicates that it is remains necessary to conduct a comprehensive analysis of industrial policies. The marginal contribution of this paper is as follows:Based on the financial subsidy policy of China's new energy auto industry, this paper empirically studies the incentivization effect of R&D subsidies and production subsidies on the innovation of new energy auto companies and the difference between the two subsidies. Based on the data of 88 listed automobile manufacturers from 2001 to 2015, this paper performs a staged regression and counterfactual estimation. The results demonstrate that R&D subsidies have obvious incentives for R&D behavior of new energy auto companies, and the effect of the incentives of production subsidies on the R&D behavior of new energy auto companies are not obvious; the net effect of the production subsidy stage is estimated to be 25.47% of the R&D subsidy stage，and the intensity of the R&D subsidy stage is lower than is that of the stage of production subsidy, but the effect of subsidies is greater than is the stage of production subsidies, and the marginal effect of subsidies' intensity for corporate R&D activities is decreasing.