Abstract: A 3-D water temperature model in the framework of MIKE3 was developed in this study to simulate the thermal stratification in the Jinpen Reservoir of Xi'an, focusing on three factors: heat exchange in the water body driven by effective diffusion and convection, inflow and outflow, and air-water heat exchange. The model parameters were determined using field measurements conducted in 2010, and the simulations were verified against field data collected in 2011. The model was applied to the predictions of different water temperature patterns in response to changes in inflow temperature or flood tunnel elevation. The simulations showed that a rise or drop in inflow temperature produced a corresponding rise or drop in hypolimnion temperature, and that releasing water through a higher dam outlet tunnel caused smaller thermocline thickness and greater temperature gradient. Thus, this water temperature model is able to reproduce with a satisfactory accuracy the stratified patterns of water temperature and their annual variations in response to hydrological and climate conditions, and it is recommended in this study for supporting the operation of the Jinpen Reservoir.