Innovative cities not only constitute an important basis for innovation activities, but also play a strategically critical role in constructing an innovative country, producing new forms of urban development, and fostering urban sustainable development. Currently, China is marching toward the goal of establishing an innovative country by 2020, but in the start-up phase of this process of innovative city construction, the fundamental transition from factor-driven development to innovation-driven development is not being realized. As a result, a wide gap currently exists between China’s innovative cities and the advanced innovative cities in developed countries. This paper argues that this necessary transition is being constrained by a series of bottlenecks in investment, income, techniques, contributions, and talents. The article takes 287 prefecture-level cities as its object of comprehensive assessment, developing a comprehensive assessment system for innovative cities and devising innovative monitoring system software in order to evaluate the current situation in China’s innovative city construction. The analysis addresses four key aspects - namely, independent innovation, industrial innovation, living environmental innovation, and institutional innovation - as well as the spatial heterogeneity of the innovative city construction process. The results demonstrate that the level of innovation in Chinese cities is low, and the paper warns that building an innovation-oriented country will, as a consequence, be difficult. Some 87.8% of the cities studied maintained comprehensive levels of innovation that were lower than the national average. The level of comprehensive innovation in a city was found to have close and positive correlation with economic development. The level of the eastern region of China was, in particular, found to be significantly higher than that of the central and western regions. The levels of urban independent innovation, industrial innovation, environmental innovation, and institutional innovation showed consistent spatial heterogeneity, as did the comprehensive level of innovation in cities. In the future, the authors suggest, China should speed up the construction process in accordance with the basic principles of “independent innovation, breakthroughs in key fields, market-oriented, regional interaction, talent-supported,” with the purpose of building up Beijing, Shenzhen, Shanghai, and Guangzhou as global innovation centers; and Nanjing, Suzhou, Xiamen, Hangzhou, Wuxi, Xi’an, Wuhan, Shenyang, Dalian, Tianjin, Changsha, Qingdao, Chengdu, Changchun, Hefei, and Chongqing as national innovation centers, by 2020. Through this process, China will finally build a national urban innovation network that includes 4 global innovative cities, 16 national innovative cities, 30 regional innovative cities, 55 local innovative cities, and 182 innovation-driven development cities, thereby contributing to the establishment of an innovative country by 2020.