Subsequent to the least cost design problem of water distribution systems (WDSs), optimal operation is probably the most explored topic. Since 1970 a variety of methods have been developed to address this problem. Although the proposed methods give theoretic ways for solving optimal operation problems of WDSs, there are little successful application cases in practice, especially when the methods were used to large scale WDSs due to too many decision variables. In consideration of using fewer decision variables, the two-level optimal method is adopted in this paper. By abstracting pump stations into high level reservoirs, the water distribution system hydraulic model can be modified into a modality, which can be used in first optimal level of two-level optimal method. Also, by building on feasible pump combination database, a new optimal method in the second optimal level will be proposed, and the proposed new method in the second optimal level will be embedded into the first optimal level, so that the problem of results discordant in different levels will be solved. By introducing new concepts and improving present optimal methods, a more practical optimal operation method of water distribution system will be established. By applying in a large scale practical water distribution system, the proposed method has been evaluated.