Abstract: The paper introduces a transcendental logarithmic production function and use panel data of industrial companies with annual revenue of more than 20 million Yuan in 30 provinces of China from 2009 to 2020, to demonstrate the influence path of R&D resource allocation distortion on provincial innovation performance at the theoretical level, and analyze the moderating effect of R&D mode and entrepreneurship. The research finds that distortion of R&D resource allocation not just negatively affects provincial innovation performance, it has different influence mechanisms at different stages of economic development; the influence curve of R&D personnel allocation distortion and R&D capital allocation distortion on provincial innovation performance show an inverted U-shaped curve and a positive U-shaped curve respectively, and the effects of both on provincial innovation performance are in an upward stage at present; R&D mode and entrepreneurship have a significant moderating effect on the distortion of R&D resource allocation and provincial innovation performance.