A comprehensive understanding of the relationship between public transportation supply and demand is crucial for the construction and sustainable development of urban transportation. Due to the spatial and networked nature of public transportation, revealing the spatial configuration and structural disparities between public transportation supply and demand networks (TSN and TDN) can provide significant insights into complex urban systems. In this study, we explored the spatial configuration and structural disparities between TSN and TDN in the complex urban environment of Beijing. By constructing subdistrict-scale TSN and TDN using urban public transportation operation data and mobile phone data, we analyzed the spatial characteristics and structural disparities of these networks from various dimensions, including global indicators, three centralities, and community structure, and measured the current public transportation supply and demand matching pattern in Beijing. Our findings revealed strong structural and geographic heterogeneities of TSN and TDN, with significant traffic supply–demand mismatch being observed in urban areas within the Sixth Ring Road. Moreover, based on the percentage results of supply–demand matching patterns, we identified that the current public transportation supply–demand balance in Beijing is approximately 64%, with around 18% of both excess and shortage of traffic supply. These results provide valuable insights into the structure and functioning of public transportation supply–demand networks for policymakers and urban planners; these can be used to facilitate the development of a sustainable urban transportation system.