In this study, in order to reveal the hydrodynamic characteristics and water quality evolution law of Water Diversion System from Hanjiang to Weihe River project Huangjinxia and Sanhekou reservoirs in the water source area and the tunnels in the water transmission area were selected. By using MIKE software to establish a hydrodynamic and water quality mathematical model, the topological structure of the water transfer system was analyzed, the hydrodynamic conditions and pollutant migration and transformation process of the study area were simulated, and the hydrodynamic characteristics of the system and the evolution law of water quality were revealed. The results are as follows. (1) The hydrodynamic simulation results show that the different typical annual average velocity in the Huangjinxia reservoir area decreases from 0.173m/s at the end of the reservoir to 0.025m/s at the front of the dam, showing a decreasing trend. The inlet velocity of the Huangsan section of the tunnel is 0.959m/s, and the velocity increases to 1.590m/s when the inflow into the Sanhekou water source area. (2) From the distribution characteristics of NH3-N, COD and TN concentrations, it can be seen that the water quality of the water transfer system has improved along the water transfer route, from the end of Huangjinxia reservoir to the exit of the water transfer tunnel. The average annual concentrations of NH3-N, COD and TN decreased from 0.248, 11.211 and 2.308mg/L to 0.241, 11.059 and 2.076mg/L, respectively. Among them, after the inflow from Sanhekou reservoir area was collected at Sanhekou control sluice, the concentrations of NH3-N, COD and TN were reduced to 0.202, 9.966 and 1.215mg/L, respectively, and the water quality was significantly improved.