A model-free sewer-WWTP integrated control was proposed. A dynamic discrete control based on the water level was developed. The approach could improve the sewer operation against flow fluctuation. The approach could increase transport capacity and enhance pump efficiency. This study aims to propose a multi-point integrated real-time control method based on discrete dynamic water level variations, which can be realized only based on the programmable logic controller (PLC) system without using a complex mathematical model. A discretized water level control model was developed to conduct the real-time control based on data-automation. It combines the upstream pumping stations and the downstream influent pumping systems of wastewater treatment plant (WWTP). The discretized water level control method can regulate dynamic wastewater pumping flow of pumps following the dynamic water level variation in the sewer system. This control method has been successfully applied in practical integrated operations of sewer-WWTP following the sensitive flow disturbances of the sewer system. The operational results showed that the control method could provide a more stabilized regulate pumping flow for treatment process; it can also reduce the occurrence risk of combined sewer overflow (CSO) during heavy rainfall events by increasing transport capacity of pumping station and influent flow in WWTP, which takes full advantage of storage space in the sewer system.