Currently, with the in-depth promotion of new urbanization and regional coordinated development strategies, megacities (clusters) with strong driving capabilities have emerged in China, posing urgent demands for building a multi-level rail transit system to better serve the transportation needs of cities (clusters). By taking into account representative megacities (clusters) such as Guangzhou, Chengdu, and Beijing hubs, this study summarizes the current status of multi-level rail transit in China and proposes main problems it faces. Development paths for enhancing the urban service function of multi-level rail transit are proposed, including promoting multi-network shared stations, emphasizing the integration of railways into core urban areas, encouraging the efficient utilization of corridor resources to achieve complementary functions and optimal economic outcomes, adhering to public transportation-oriented operation, and increasing railway network supply to achieve the connection and integration of national railway and subway networks. Taking Beijing as an example, a planning scheme is presented to enhance the urban service function of multi-level rail transit. On this basis, it is suggested to innovate development concepts from the aspects of improving hub connectivity, optimizing the layout of production facilities, leveraging the integration effect of transportation stations, focusing on the utilization of existing corridor resources, and further promoting public transportation-oriented operations. It is also necessary to strengthen practical exploration to accumulate experiences for further improving the service and support capabilities of rail transit for urban development.