Abstract Resource-based cities face vital economic, social, and environmental problems during their industrial transformation. Urban industrial structure is a traditional primary industrial pattern, which is resource-based and resource-intensive economy with low level technology and efficiency. They encounter tremendous pressure of unemployment and social security. Resources of such cities are on the verge of extinction, in addition, the environmental pollution and ecological conditions are becoming worse. The cities have significant institutional issues and their innovation capacity is inadequate. Therefore, it is necessary to carry out strategic innovations to realize the successful economic transformation of resource-based cities. The strategic innovations include innovation of development goals, equalization of social welfare, sustainable economic development, coordinative development between eco-environment and socioeconomy, and circular economy development strategies optimizing diversified industrial structures. In addition, forming eco-industrial system and changing traditional growth pattern, strategy of resource and industrial substitution and supplement, scientific and technological innovation strategy —late-comer's advantages of development of new high-tech ecocity development strategy and innovation of institutional mechanism and systems.