As a typical fast-growing plain city with the title of “city of hundreds of lakes”, Wuhan, Hubei Province in China, boasts abundant regulating and storing water space. However, this city has suffered from frequent waterlogging and unbalanced storage due to rapid urbanization. To tackle the issue, this study inspired by the idea of “Nature-Based Solutions” (NBS). Taking the major drainage system of Wuhan as an example, it explored the identification and construction of storage and drainage area as well as the planning strategies in the city scale, based on a sustainable urban stormwater system cycle compatible with artificial deployment and natural stormwater process. The stormwater process is simulated with numerical inverse method. Then the drainage network and the natural force get a balance in the system. The result showed that: 1) With the SCS-CN model and surface equal volume filling method, the spaces storing excess surface runoff were identified under the geography and storm recurrence interval; 2) Combining the data of construction land, actual submergence area, and waterlogging points, the major drainage system with emphasis on the restriction of surface elevation were organized. 3) The “storage and drainage function area of major drainage system” was proposed as a NBS. The hierarchical distribution was adopted for layout optimization of urban land use in Wuhan—include the area of storage and drainage, area of strengthened self-drainage, area of waterlogging reduction, and area of low intensity development. Furthermore, it also offered references to the identification and improvement of waterlogging risk points of public facilities in built area.