Digital innovation is profoundly reshaping the spatial configuration of innovation networks; however, the diffusion patterns and underlying drivers of inter-city digital innovation in China remain under-explored insufficiently examined. Drawing on digital patent data from 292 cities between 2005 and 2020, this study constructs an inter-city digital innovation network using an improved gravity model and applies complex network analysis together with a TERGM approach for empirical assessment. The findings show that: (1) the network has expanded rapidly, reaching 265 nodes and 3,493 edges, and has formed an “east-dense, west-sparse” spatial structure with heterogeneous characteristics across four major urban agglomerations; (2) trunk diffusion has accelerated, resulting in a multi-centered system led by Beijing and supported by multiple secondary hubs, while emerging nodes such as Kunming and Nanning began to integrate into the trunk after 2010, accompanied by exponential growth in trunk connectivity; and (3) urban economic development and community structure significantly promote diffusion. Moreover, industrial similarity in the digital innovation sector improves cooperative efficiency by a factor of 4.1, whereas similarity in industrial advantage suppresses diffusion by 50.4% per unit due to intensified intra-industry competition. Overall, this study reveals the evolutionary dynamics of China’s inter-city digital innovation network and provides scientific insights for formulating differentiated innovation policies, optimizing resource allocation, and unlocking the potential of digital innovation to support high-quality economic development.