Antimicrobial resistance genes (ARGs) are widespread across various regions. While several studies have investigated the distribution of antibiotic resistance in natural environments, the occurrence and diversity of ARGs in the Three Gorges Reservoir have not been fully elucidated. In this study, we employed metagenomic sequencing techniques to investigate the abundance, diversity, and influencing factors of ARGs in the ecosystem of the Three Gorges Reservoir. A total of 874 ARGs, 20 antibiotic classes against which resistance genes are deployed, and 6 resistance mechanisms were detected. The dominant ARG is the macB gene, the dominant antibiotic class is multidrug resistance (MDR), and the dominant resistance mechanism is antibiotic efflux. The microorganisms with the highest contribution to ARGs are Betaproteobacteria and Gammaproteobacteria, while physicochemical factors have little impact on the distribution of ARGs. The results indicate that the Three Gorges Reservoir constitutes a significant reservoir of ARGs. By examining the distribution of ARGs in the sediments of the Three Gorges Reservoir and the associated characteristics between microorganisms and ARGs, we aim to understand the current state of resistance pollution in the Three Gorges region, thereby providing theoretical support for risk assessment of resistance genes in the environment.