Based on SWAT-EFDC model, ecosystem service value assessment method and cooperative game theory were applied to conduct a comparative analysis of ecological compensation standards for inter-basin water diversion project of Qincun Reservoir. The results show that, water resource volume at dam site of Qincun Reservoir decreased from 254 million m³ in baseline scenario to 128 million m³,and water resource volume at outlet of downstream basin decreased from 420 million m³ to 294 million m³. Pollutant carrying capacity of COD Mn and NH₃-N in upstream reservoir area decreased by 43.66% and 42.68%, respectively, while that in downstream river channel decreased by 40.67% and 18.57%, respectively. Upper limit of ecological compensation for water source area calculated by ecosystem service value assessment method is 241 million yuan, and total ecological compensation for water receiving area determined by cooperative game theory method is 204 million yuan, including 159.32 million yuan for water source area and 44.19 million yuan for downstream area.