—Taking Five Economic Zones of Sichuan Province as an Example

In order to explore the regional innovation efficiency of collaborated five major economic zones in Sichuan Province, as well as the inner gaps in development, this paper collected data from 21 prefecture cities, including 18 prefecture level cities and 3 autonomous prefectures, and used Three-stage DEA model to evaluate the innovation efficiency under environmental controls. Result shows that excluding the environmental factors makes it more possible to assess the innovation efficiency accurately; among the prefecture cities in the five major economic zones, Chengdu and Panzhihua are at the forefront of efficiency, while the other prefecture cities need to improve their pure technical efficiency and scale efficiency. The research process and conclusions of this study can provide a reference for the measurement of regional innovation efficiency from the perspective of prefecture-level city.