Ecological security (ES) is an important element in the construction of an ecological civilization and plays a vital role in ensuring the sustainable development of social economies. Further, ES is an important measure of regional sustainable development. Based on ecosystem theory, this study constructs a comprehensive evaluation framework using the driving force-pressure-state-impact-response (DPSIR) and slacks-based measure of data envelopment analysis (SBM-DEA) models. Taking the Three Gorges Reservoir Area as an example, the study develops an ES evaluation system and realizes a transformation from “efficiency” to “quality”.Gray correlation theory and spatial autocorrelation and are adopted to analyze the ecosystem's spatial–temporal evolution and driving factors. The results demonstrate that the overall level of ES in the Three Gorges Reservoir Area from 2010 to 2020 was good; however, the spatial distribution of ES revealed an unbalanced state. The influence of each subsystem on the result of the ES evaluation is state > response > impact > driving force > pressure. The spatial correlation analysis of ES in the Three Gorges Reservoir area exhibited a positive autocorrelation, and the agglomeration effect was significant; on this basis, the key factors affecting ES were identified. The ratio of environmental protection investment, sewage treatment rate, green coverage rate of built-up areas, proportion of primary industry in GDP, and proportion of tertiary industry in GDP had notable effects on the ES of the study area. The research contributes to the theory of ES and provides guidance for ecologically sustainable development.