The understanding of the impact of different government support methods on R&D efficiency is of great significance for evaluating the performance of innovation policies in various countries. We selected 31 manufacturing industries in China from 2009 to 2015, used the stochastic frontier analysis (SFA) method to measure R&D efficiency, and used tobit regression method to examine the relationship between direct government subsidies and preferential tax policies and manufacturing R&D efficiency. The results reveal that the overall R&D efficiency of China’s manufacturing industry was low, but it has been steadily increasing, and the R&D efficiency of emerging industries was significantly higher than that of traditional industries. Tax incentives played a stable and significant role in promoting R&D efficiency in manufacturing. Affected by factors such as the government’s long-term preference and information asymmetry, direct subsidies had no significant impact on the current R&D efficiency of the manufacturing industry, and began to play a positive role after a two-year lag. Based on the above research findings, this paper suggests that progressive preferential tax rates can be designed according to the “base + increment” approach for tax preferential policies. At the same time, different proportions of tax cuts should be set for enterprises of different sizes and levels of innovation, and the focus should be on small and medium-sized enterprises and emerging industries. In terms of direct funding subsidies, the government should not only increase the support for basic research, but also give more preference to enterprises that receive tax incentives for research and development, so as to enhance the complementary effect of the two types of subsidy policies. The marginal contribution of this paper mainly includes three aspects: First, based on the Chinese situation, the impact of direct government subsidies and tax incentives on the R&D efficiency of the manufacturing industry is tested. Second, we present the evidence that direct government funding subsidies “crowd out” enterprise R&D funds. Thirdly, we describe the influence of enterprise scale, innovation level, ownership, and management ability on R&D efficiency of the manufacturing industry, and put forward the possible influence mechanism.