This study investigates the dynamics of innovation element flows among metropolitan areas and examines the underlying proximity mechanisms that are crucial for elevating urban agglomerations’ innovation levels and spurring their development. Utilizing collaborative publication and patent data, this research constructs knowledge and technological innovation networks within the Nanjing metropolitan area (NMA) from 2013 to 2020. It analyzes the evolution of network structures and applies the Multiple Regression Quadratic Assignment Procedure to discern the proximity mechanisms driving the urban innovation networks’ evolution in NMA. The main findings are as follows: (1) The knowledge collaborations within NMA cities remain largely confined to cities within Jiangsu province, whereas the technological collaborations are shifting from intra-province to cross-province cooperation. (2) Both knowledge and technological innovation networks display a “core-periphery” configuration, with Nanjing maintaining a dominant central position. The scale of the KIN surpasses that of the TIN, while the latter’s growth rate outpaces the former’s. Technological collaborations demonstrate more pronounced spillover effects than their knowledge counterparts. (3) At the metropolitan area level, organizational, social, cognitive, and technological proximities exert varying degrees of influence on innovation cooperation among different innovation entities across various years. Cognitive proximity exhibits the most substantial explanatory power. Based on these findings, the study proposes relevant policy recommendations for constructing an innovative NMA and promoting collaborative innovation development among cities within the NMA.