From the perspective of pollution load allocation, the key to the total amount control of pollutants, this paper studies the optimal allocation scheme of pollution loads under the synergistic influence of point and non-point sources in the plain river network area with a complex water system. In this study, the concept of water quality compliance rate was introduced, and the random analysis method, combined with the hydrodynamic and water quality mathematical models, was used under the deterministic rainfall runoff and pollution load from point and non-point sources. Following the principles of fairness and feasibility, a non-linear optimal allocation model for point and non-point source pollution loads was developed based on the water quality compliance rate of multiple control sections, with satisfaction of the environmental control requirements of pollution sources and technical parameters of pollution control as constraints and the maximum allowable emissions of pollutants as the objective function. A case study of a river network area in Taihu Lake was conducted to verify the model. After optimal allocation of pollution loads from point and non-point sources in this area, the guarantee rates of ammonia nitrogen and total phosphorus concentrations in each control section to attain the water quality standard could reach 90% over the whole year. Results show that the proposed model can effectively realize the optimal allocation of pollution loads from point and non-point sources in the plain river network area, and improve the global management efficiency of regional pollutants.