Building an innovative city is not only of great significance to the implementation of the national innovation strategy, but also can further enhance the internal driving force of regional economic development. As the youngest municipality directly under the central government, Chongqing City provides a basis for systematically identifying and accurately recognizing the current situation of urban innovative ability, and further provides a basis for formulating urban innovation development strategy, and the author proposes to construct an appropriate innovative indicator system to comprehensively evaluate the urban innovative effect. Through the comprehensive evaluation method, this paper takes the data of Nanan District of Chongqing from 2008 to 2017 as a sample to construct an innovative urban indicator system, and conducts an empirical research on the seven categories of secondary indicators, namely, demand innovation, factor innovation, industrial innovation, environmental innovation, institutional innovation, organizational innovation and stylistic innovation. The conclusion shows that factor innovation has entered a depressed economic cycle, environmental innovation has not received much attention, and organizational innovation has stagnated. In this regard, the government should give full play to the advantages of demand, make rational use of factor resources, advocate green and sustainable environment, and change the way of organizational innovation.