In order to not only solve the technical problems of quantifying the degree and range of the effect that is caused by the water quality of upstream on that of downstream portions of a river, and of dividing the responsibility of transboundary water pollution, but also to tackle the difficulty in adapting to dynamic changes of the traditional water quality model in terms of practical application, pollutant discharge and water consumption were taken as the main influence factors to build the transboundary water quality transfer effect model. Supported by a comprehensive integration platform, the transboundary water quality transfer effect simulation system of the Yellow River mainstream was constructed. The simulation results show that the concentration decreases exponentially along the range. Gansu, Ningxia, and Inner Mongolia had a more significant effect of exceeding standard water consumption on pollution, while Ningxia, Inner Mongolia, Shaanxi, and Shanxi had a more distinct contribution to the over standard pollution discharge effect. The proposed model and simulation system can provide new methods and instruction for quantifying the degree and range of transboundary water pollution, as well as dividing the responsibility for water environment compensation.