Abstract: The total discharge control of pollutants is the core of the environmental regulation, which has greatly improved the environment and enabled sustainable development. In this paper, the deficiencies in the application of the total pollutant load control system were analyzed from the angles of the science foundation and system design. Furthermore, the corresponding suggestions were proposed to contribute to improve the efficiency of the total pollutant load control system, which covered the aspects of the science and technology development, cooperative binding force, coordinating mechanism and economic means.