Based on the panel data of 21 cities (prefecture-level cities) in Sichuan Province from 2011 to 2018, the SBM-Malmquist model is used to measure and compare the change of S&T innovation efficiency and innovation productivity. The research results show that the technological innovation efficiency of 21 cities (prefectures) in Sichuan Province is relatively low from 2011 to 2018, and generally shows a trend of first decreasing and then increasing. The scientific and technological innovation efficiency of five economic zones in Sichuan Province is obviously different from panxi economic zone, Chengdu Plain economic zone, northwest Sichuan ecological economic zone, northeast Sichuan economic zone and south Sichuan economic zone in descending order. The change of overall innovation productivity showed an upward trend, and the change of innovation productivity in all cities and states showed regional concentration, and so on the change trend of neighboring cities . According to the above research results, countermeasures and suggestions are put forward from three perspectives: government fiscal and tax subsidies, introduction of skilled talents, and strengthening of intellectual property protection, in order to provide beneficial enlightenment for regional optimization of scientific and technological resources allocation.