The phase delay of water surface evaporation compared to meteorological factors such as net radiation in seasonal changes reflects the impact of water heat storage on water surface evaporation. Quantifying the hysteresis response of this fluctuation to meteorological factors is crucial for understanding and estimating evaporation in deep reservoirs (lakes). The water level and area of river type deep-water reservoirs such as the Three Gorges Reservoir have significant periodic changes. However, the understanding of the intra-annual hysteresis effect of water surface evaporation is still limited. In this paper, the seasonal variation of water surface evaporation and its intra-annual hysteresis effect were analyzed by using the evaporation and meteorological observation data of the water surface evaporation site and the land surface evaporation site in Badong Station of the Three Gorges Reservoir from August 2013 to July 2020. The results show that the evaporation rate of the water surface evaporation site shows a bimodal pattern in December and August within a year, which is significantly different from the unimodal pattern in August for the land surface evaporation site. The hysteresis time of water surface evaporation relative to net radiation, average temperature and water surface temperature was 4, 3 and 2 months, respectively, while the relative hysteresis time of land surface evaporation was less than 1 month. Compared with the land surface evaporation site, the hysteresis time between water temperature, evaporation and water surface and atmospheric saturation difference was 1, 3 and 4 months, respectively, while there was no hysteresis between average temperature and net radiation. This paper revealed that the intra-annual hysteresis effect of water surface evaporation in the Badong Station of the Three Gorges Reservoir was mainly affected by the seasonal hysteresis of the saturation difference between the water surface and the atmosphere caused by the water temperature of the reservoir. It is necessary to clarify the water surface evaporation characteristics of the entire Three Gorges Reservoir by in-depth analysis of the temporal and spatial changes of water temperature under reservoir operation.