Enterprise innovation efficiency is the key issue affecting the innovation ability of Chinese enterprises. The internal shareholding structure has a direct impact on the innovation efficiency of enterprises. Based on the data of Chinese listed companies in 2008-2017, based on the three-stage DEA model, based on the control of external environmental factors, Investigated the mechanism of the ownership structure on the efficiency of technological innovation of listed companies in China. The research shows that: (1) The efficiency of technological innovation of listed companies in China is generally low, and the average value is below 0.7. After removing environmental factors and random interference factors, the comprehensive technical efficiency value is improved before the elimination, indicating that the innovation efficiency of the enterprise is affected. The adverse environmental impact is not because their management level is low. (2) Environmental factors have a significant impact on the efficiency of technological innovation of enterprises. Government subsidies, foreign investment, and the establishment of enterprises are conducive to enterprise innovation. The higher the degree of competition in the industry and the greater the number of enterprises in the region, it is not conducive to the efficiency of technological innovation. (3) The shareholding of large shareholders and the efficiency of technological innovation of enterprises are not monotonously increasing or decreasing, and there is an inverted “U” relationship. The balance of ownership has a negative impact on the efficiency of technological innovation of enterprises. Institutional investors have a positive effect on the efficiency of technological innovation of enterprises. State-owned enterprises and private enterprises, whether in the shareholding of large shareholders or the balance of equity, the efficiency of technological innovation of enterprises There is no significant difference in the effect.