According to the red line of emission control of water pollutants, and the basin total emission quantity control allocation practice in China, this paper established a combined multi-factor allocation model for initial basin emission rights allocation in the principle of total emission control of water pollutants, the balance of fairness and benefits, respect for the difference of regional water environment, and guarantee of the continuous development of society and economic. From the perspective of the configuration model's focus and function, a comparison analysis was made with the current economic activity allocation model, non-economic factor allocation model and the discharge performance allocation model. The research results taking Taihu Basin as an example showed that multiple hybrid allocation mode aggregated the advantages of the variety of configuration patterns, and it is closed to the water-environmental-capacity allocation mode, It has realized the effective decomposition of the total emission control of basin water pollutants. At the same time, it is beneficial to promote economic growth and social justice with moderately increasing the amount of the initial emission permits of COD and NH3—N and TP in Jiangsu province and Shanghai city. Meanwhile, this allocation mode is convenient to operate and spread.