The safety of water quality in the Three Gorges Reservoir (TGR) is very important. Protections and remediation of environment safety are very crucial for guaranteeing TGR environmental quality. When piled municipal solid waste (MSW) dumps are submerged without treatment, pollutants in the MSW will leach into the water and threaten the water safety of the reservoir. Based on the surveys of the amount, distribution and characteristics of piled MSW in the TGR area, this study focusing on the MSW dumps at the water level between 135 m to 175 m, proposed a "cleaning plan" for these dumps. After the dynamics simulation and scale-up experiments, a source density model was put forward. This 2-dimenstionai water quality model was used to analyzed the impacts of piled MSW on the water quality safety in the reservoir. The results show that these dumps will potentially threaten the safety of TGR water quality if submerged without proper treatment. Given the proposed cleaning plan implemented before water storage, the added concentration of COD will be less than 0.03 mg/L. This plan will surely protect the safety of the reservoir.