Ertan Hydroelectric Power Station was the first large-scale water conservancy facility in western China, and with its completion, the ecological pattern of the reservoir area has changed dramatically; however, the changes in habitat quality before and after the completion of the reservoir have not yet been systematically monitored and evaluated. In this study, we analyzed the spatial and temporal characteristics of the remote sensing ecological index (RSEI), used CA-Markov model and GeoDetector, evaluated the ecological environment of the Ertan Reservoir area in each five-year period from 1995 to 2020, simulated the ecological quality of the Ertan Reservoir area in 2025, and revealed the nine drivers and their interactions affecting ecological quality of the watershed from a geologic point of view, and finally put forward reasonable planning and targeted protection suggestions. Finally, rational planning and targeted protection recommendations were proposed. The main results were as follows: (1) After the completion of the Ertan Hydropower Station, the spatial distribution of the RSEI in the reservoir area varied significantly, with a trend of “rising-declining-rising” in time, and the area share of “good” area increased the most, by 19.83%. (2) The degree of grading of each driving factor had different degrees of influence on the size of the RSEI value, and its interaction enhanced the spatial differentiation of the RSEI. (3) The average value of the RSEI is 0.66 in 2025, and the ecological environment quality will show a steady improvement in five years. The results of the study can provide a reference for constructing RSEI indicators for large hydropower facilities.