The discharge of low-temperature water from the middle and lower layers of thermally stratified dam reservoirs leads to thermal pollution and adversely affects fish production and reproduction in downstream rivers. Selective water withdrawal using stoplog gates is an effective approach to address this issue. However, comprehensively and effectively evaluating the effects of stratified withdrawal and optimizing the scheduling of stoplog gates to provide better ecological services to downstream habitats pose significant challenges for reservoir managers. In this study, an equivalent elevation method (EEM) was developed based on in situ observation data of water temperature. The EEM calculates the equivalent withdrawal elevation (EWE) in the far dam area corresponding to the discharge-water temperature (DWT), facilitating the evaluation of stoplog-gate effects. EEM was applied to a thermally stratified dam reservoir in southwestern China (Guangzhao reservoir, GZ). The results showed a significant positive correlation (r > 0.7, p < 0.05) between DWT and the vertical-water-temperature structure in the far dam area. The average EWEs for the 5-layer, 4-layer, and 3-layer stoplog gates in GZ were 697.2 m, 690.8 m, and 689.9 m, respectively. Utilizing the EEM findings, a scheduling operation scheme was proposed to improve DWT while reducing the number of stoplog-gate operations, thereby increasing their efficiency and saving the cost of invested labor and time. This method provides a reference for reservoir managers in optimizing stoplog-gate-scheduling strategies to mitigate potential risks to aquatic ecosystems caused by abnormal water temperature.