Based on the panel data of 30 provinces（due to the lack of data, the statistical data mentioned here do not include the Tibet Autonomous Region, the Hong Kong Special Administrative Region, the Macao Special Administrative Region and Taiwan Province） in China from 2010 to 2020, the three-stage DEA model was used to measure the efficiency of fiscal science and technology expenditure, and the entropy method was used to measure the regional innovation capacity. Finally, the system GMM model was constructed to figure out the relationship between them. The results show that there is heterogeneity in the influence of different types of fiscal science and technology expenditure efficiency. The research output efficiency has an inverted U-shaped influence on regional innovation capacity, while economic output efficiency has a significant positive impact on regional innovation capacity. Human capital negatively moderates the inverted U-shaped relationship between scientific research output efficiency and regional innovation ability, but positively moderates the relationship between economic output efficiency and regional innovation ability.