In order to study the effect of water diversion project operation on the hydrodynamics and water temperature structure of the Hedi reservoir , a three-dimensional hydrodynamic water-temperature coupling model was established based on MIKE3, and the changes of hydrodynamic, water temperature structure and stability of Hedi Reservoir under different scenarios were analyzed by combining the relative water column stability(RWCS). The results show that the high-flow diversion and drainage after the operation of the water diversion project significantly enhance the original hydrodynamic conditions of Hedi Reservoir, and the low operating water level is the most affected by the water diversion due to the small flow in dry years. The hydrodynamic enhancement caused by the inflow of external water will intensify the mixing between water bodies, resulting in a uniform vertical water temperature distribution, and the greater the increase in hydrodynamic force, the greater the damage to the water temperature structure. The change of water temperature structure will cause the change of water intake water temperature, which will have an impact on the irrigation area and downstream ecology. The operation of water diversion project will reduce the stability of thermal stratification of Hedi Reservoir, which will help weaken the water quality stratification formed by water temperature and thermal stratification in summer and autumn.