This paper calculates the inter-provincial science and technology innovation capital efficiency, total factor productivity and its decomposition index by using relevant data of 30 provinces in China from 2009 to 2017. The results show that the total factor productivity growth of national science and technology innovation mainly comes from the change of technological efficiency. The efficiency of resource allocation in the eastern region is high, and the improvement of total factor productivity mainly comes from technological progress; the increase of total factor productivity in the western region is large, and the change of technological efficiency is the main driving force. Further，Tobit regression shows that government support, openness, industrial structure, human capital and total factor productivity are significantly related. Finally, this paper puts forward some countermeasures and suggestions.