Innovation-driven development provides new impetus for economic and social development and is the core approach to leading future economic transformation. Government R&D investment reflects the national will, and it is necessary to evaluate its output efficiency. Using panel data from 31 provinces(due to the lack of data, the statistical data mentioned here do not include the Hong Kong Special Administrative Region, the Macao Special Administrative Region and Taiwan Province) in China from 2018 to 2022, 13 specific indicators from the input and output sides were selected to build a performance evaluation system for government R&D investment. Factor analysis was used to study the government R&D investment performance. Combining the model construction and the results analysis, improving government R&D investment performance is proposed by promoting diversification of R&D funding sources, optimizing the execution structure of government R&D funding, and increasing R&D personnel input.