The accounting model of green economy growth based on production frontier theory not only considers technological inefficiency and environmental cost but also is consistent with “materials balanced approach”. In this model, the sources of economic growth are decomposed into such three parts as technological progress, technological efficiency change and capital deepening under the restriction of environment. The empirical analysis results of Chongqing’s 27 manufacturing industries indicate that there was technological inefficiency widely during economic growth, but over 50% industries’ technological efficiency is improved or remains unchanged and that capital deepening dominates the sources of economic growth, but the contribution of total factor productivity change dominated by technological change is relatively less and technological progress is the main reason for the growth of total factor productivity. In order to bring potential capability of sustainable development of Chongqing’s manufacturing industry into full play, the economic development pattern must be changed in the future, and Chongqing should choose the way of green total factor productivity growth by considering both technology progress and technological efficiency improvement under the binding of environment.