Modern megalopolis is a critical spatial unit for the construction of urban agglomerations. With the national aims to facilitate a robust transportation network, the integration of multiple rail networks including national (high-speed) rail, intercity railway, suburban railway, and urban rail transit, has become one of the effective strategies to meet the transportation needs at different levels and scopes. There is still a lack of attention to study the supply mechanism and multi-level governance of the suburban rail investment and development in China. As the multi-level governments continue to strengthen the accessibility and connectivity between the central and the peripheral areas, it has become essential to optimize the network planning, financing mechanism, and spatial governance of diverse suburban railway system. By taking the suburban rail in the megalopolis of Zhejiang province as an example, this paper adopts text analysis and critical group interviews—with a special focus on main case—to identify three typical different suburban rail mechanisms and their particular characteristics in the financing, operating and spatial governance. The results show that: 1) The construction mechanism of suburban rail has diversified regional embeddedness. 2) As an essential link to promote the integration of multiple rail networks under modern megalopolis, the multi-modal suburban rails have presented diversified financing and operation advantages. 3) The multi-level collaboration is a significant basis for the supply of multi-modal suburban rails in the stages of approval, financing, construction, and operation, showing complicated, dynamic, and multi-level territorial relations. By doing so, it has specific theoretical and practical implications for a better understanding of suburban rail planning and construction and their socio-economic effects under the rapidly urbanizing China.