Abstract: This paper firstly estimates high technology industry innovation efficiency of China's 30 provinces from 2008 to 2013 using stochastic frontier model based on transcendental logarithmic production function, and then researches the relationship between the enterprise scale, market structure, government investment, the impact of R&D expenditure structure with the innovation efficiency based on geographical weighted regression model. The results show that: there is positive correlation between high technology industry innovation efficiency among China's 30 provinces; enterprise scale, market structure and R&D expenditure structure have a positive impact on innovation efficiency, and government investment hinders innovation efficiency of high technology industry; influence on the innovation efficiency of the high technology industry by four factors all have spatial heterogeneity, and keep stable from 2008 to 2013. Finally this paper makes conclusions and puts forward relevant policy suggestions.