As the digital economy expands, data has become a key production factor shaping economic growth and technological progress, and an important medium linking knowledge flows across cities. Using patent citation data for 275 Chinese cities from 2010 to 2022, this study examines how data factors influence intercity knowledge flows. The establishment of National Big Data Comprehensive Pilot Zones serves as a quasi-natural experiment, and social network analysis is applied to construct urban innovation networks and uncover the underlying mechanisms. Results show that the pilot zones significantly strengthen cities’ knowledge absorption and diffusion abilities and promote intercity knowledge flows by enhancing collaborative innovation. The effects also differ across cities occupying different positions in the innovation network. These findings deepen the understanding of how data factors shape knowledge flows and offer policy insights for building a data-factor market, improving innovation networks, and advancing regional knowledge governance in the digital era.