Abstract: An increasing number of studies confirm that there is a mutually reinforcing relationship between innovation development and high-skilled labor agglomeration within cities. Between cities, however, the relationship between innovation collaboration and the migration of high-skilled labor has not been fully revealed, especially with stronger urban connections and the growing importance of network capital. This study selects 337 prefecture-level and above administrative regions across China, excluding Hong Kong, Macao and Taiwan. It constructs a dual-layer network of ‘high-skilled labor migration-intercity innovation’ using microdata from the 2015 population sample survey and patent data from 2011 to 2015. The interaction between intercity innovation and high-skilled labor migration networks is empirically examined using Quadratic Assignment Procedure regression and Exponential Random Graph Model, with a focus on two aspects: overall network development and internal network self-organization. The research findings reveal that, in the overall development of both networks, the flow of highly skilled labor promotes the development of intercity innovation networks, which in turn encourage labor migration. With regard to network self-organization, the development of both networks is driven by local interactions between migration and innovation networks. This interaction is not limited to directly connected cities but also enables cities with no direct links to establish innovation or migration relationships through the effect of third-party cities transmitting resources or information. The results confirm a mutual reinforcement between intercity innovation and skilled labor migration, suggesting cities should seize innovation collaboration opportunities, attract skilled labor, and create feedback loops to enhance network capital.