At present, environmental issues associated with rapid economic development are becoming critical concerns that arouse government’s and people’s particular attention. A large amount of influencing factors and especially their complicated interactions have always thrown confused insights into assessing the dynamic evolvement and sustainable development of urban economy–resource–environment (ERE) system and programming the developing strategies. According to connotation and framework of sustainable development, this study proposes a hierarchical multi-level method to evaluate the urban sustainability in Chongqing city of China suffering from depletion of resource and degradation of environment. Integrated assessment results indicate that the current ERE system of Chongqing is not sustainable; environment development mode is more effective to sustainable development of urban ERE system. Under the considerations of development features and regional differences, as well as regular discipline on urbanization, a coordinated combination of environmental, resource and technology modes is believed to realize sustainable development of ERE system.