How to promote and improve the level of urban innovation cooperation is a major issue in China's current high-quality economic development. Thus, enhancing innovation ability is essential to achieving high-quality economic growth under the "new normal". Based on the data of Chinese invention patents from 1985 to 2017, this paper analyzes the characteristics of China's urban innovation cooperation network and the different roles of proximity by using social network analysis and exploratory spatial data analysis methods. The analysis results show that: (1) On the whole, the development of China's urban innovation cooperation network is characterized by stages (initial development stage, rapid development stage, and gradual decline stage); The urban innovation cooperation network has strong connectivity and centripetal concentration but its imbalance needs to be further improved; The degree of urban participation has gradually increased, consolidating the stability of the network structure. (2) The centrality of urban innovation cooperation network has obvious characteristics of administrative center orientation, coastal areas orientation, and 'strong east and weak west'; Beijing is the center and bridge of the network, and the network flattening characteristics are obvious; A hierarchical 'core-edge' structure is gradually formed for the urban innovation cooperation network, and the pyramid structure with Beijing standing at the top is being consolidated. (3) The geographical proximity presents a significant global spatial positive correlation, while the network proximity and pure network proximity have a more significant global spatial negative correlation; The local spatial autocorrelation of China's urban innovation cooperation system based on network proximity is more obvious and identifiable than that based on the geographical proximity, which better reflects the new development model of "relationship economy".