With the development of the social economy and the demand for environmental protection, people's requirements for clean and renewable energy are gradually increasing. Generally, renewable energy, such as wind power and photovoltaic energy, has natural intermittency to varying degrees. Consequently, renewable energy sources, due to their fluctuating nature, cannot provide a continuous supply of power and hence require bulk electricity storage. Additionally, energy storage is important to electrical systems, allowing load levelling, peak shaving, frequency regulation, damping energy oscillations, and improving power quality and reliability. Pumped storage power stations are notable for their ability to efficiently store energy on a large scale. The construction of a reservoir inevitably changes the water temperature situation of the original river channel. The expansion of pumping and storage units on a pre-existing reservoir, namely, a mixed pumped storage power station, is different from a conventional power station in terms of the thermal structure of the reservoir area. This study focuses on the Jinshuitan hydropower station and uses the MIKE3 model to analyse the influence of different outlet elevations and pumping flows on the water temperature structure of the reservoir area. The water pumping had no impact on the surface water body but did have a significant impact on the middle and bottom water bodies. The vertical water temperature stratification intensity weakened under different pumping scenarios, and the temperatures of the middle and bottom water bodies increased. The influence of the outlet elevation on the water temperature structure in the reservoir area was much greater than that of the pumping flow. The lower the elevation of the water outlet was, the greater the impact. For the Jinshuitan hydropower station, when the elevation of the water outlet was 130 m, the water temperature of the bottom column rose significantly, the stratification intensity of the water column weakened significantly, and the reservoir reached a vertically isothermal state in December. In summary, water pumping dramatically changed the original water temperature structure in the reservoir. The final research results can provide an effective reference for follow-up studies on relevant ecological and environmental issues associated with the development of pumped storage power stations and for setting the outlet elevation and pumping flow.