Rail transit plays a crucial role in improving urban sustainability and livability. In many Chinese cities, the planning of rail transit routes and stations is focused on facilitating new developments rather than revitalizing existing built-up areas. This approach reflects the local governments’ expectations of substantial growth to reshape the urban structure. However, existing research on transit-oriented development (TOD) rarely explores the spatial interactions between individual transit stations and investigates how they can be integrated to achieve synergistic effects and balanced development. This study proposes that rail transit systems impact urban structure through two “forces”: the provision of additional and reliable carrying capacity and the reduction of travel time between locations. Metro passenger flow is used as a proxy for these forces, and community detection techniques are employed to identify the actual and optimal spatial clusters in Wuhan, China. The results reveal that the planned sub-centers align reasonably well with the optimal spatial clusters in terms of spatial configuration. However, the actual spatial clusters tend to have longer internal travel times compared to the optimal clusters. Further exploration suggests the need for equalizing land use density within planned spatial clusters served by the metro system. Additionally, promoting concentrated, differentiated, and mixed functional arrangements in metro station areas with low passenger flows within the planned clusters could be beneficial. This paper presents a new framework for investigating urban spatial clusters influenced by a metro system.