The extant literature on evaluating the influence of R&D fiscal policies primarily focused on the advantages of the input or output additionality, neglecting that excessive incentives caused by R&D fiscal policies may lead to R&D inefficiency. From the perspective of resource misallocation, this paper divides R&D inefficiency into input redundancy and output insufficiency, then further measures the impact of three typical R&D fiscal policies on R&D inefficiency based on the firm-level sample of Zhongguancun Science Park in China. A two-step empirical analytical framework is constructed in this paper, namely, the inefficiency measurement step and the influence assessment step. The results prove that R&D fiscal policies may lead to resource misallocation and aggravate R&D inefficiency, and the heterogeneous conclusions cross three policies are found. Specifically, the subsidy policy significantly promotes the increase of R&D inefficiency, which primarily reflects in the rise of input redundancy. The pre-tax additional deduction policy does not show a significant impact on the R&D inefficiency but increases the input redundancy. On the contrary, the preferential tax rate for high-tech enterprises policy effectively inhibits the inefficiency. This paper not only attempts to reveal the formation of R&D inefficiency theoretically from the perspective of resource misallocation, but also takes China as an empirical sample to provide evidence for guiding the design of more effective R&D fiscal policies.