Abstract: To investigate the fish community composition and diversity characteristics of typical riffle-pool river sections in the fluctuating backwater area of the upper Changjiang River, environmental DNA (eDNA) technology was applied to analyze fish species diversity in the Guangyangba and Dajiantan river sections. The results showed that a total of 77 fish species, belonging to 54 genera, 19 families, and 11 orders, were detected across the two sections, in which Cyprinidae fish were predominant. All the fishes included 14 endemic species of the Changjiang River and 8 exotic species. Overall, Cyprinus carpio, Ctenopharyngodon idella, and Hemiculter bleekeri were identified as the dominant species in this survey. α diversity analysis revealed higher fish species diversity in the branch channels of both sections. Additionally, fish species distribution was more even in the Guangyangba section compared to the Dajiantan section. The classification of fish ecological groups indicated that the fish in the study sections were primarily characterized by omnivorous feeding habits, preference for slow-flowing water, mid-to-bottom layer activity, non-migratory behavior, schooling tendencies, and adhesive egg-laying. This study demonstrates the effectiveness of eDNA technology in revealing fish species diversity and ecological group information. It provides targeted recommendations for the conservation of fish diversity in the Changjiang River and offers scientific support for the design of river restoration projects.