Reservoirs are important artificial ecosystems that modify the hydrological and ecological characteristics of a river. Knowledge of the basic characteristics of fish assemblages in reservoirs is a first step toward the development of effective conservation policies. We used the information collected over a 10-year period (2006-2015) to assess the structure of the fish assemblages in the Three Gorge Reservoir (TGR) in a river-dam gradient. Three fish zones were detected in TGR. Species richness was the highest in the upper zone and lowest in the lower zone. The riverine zones were dominated by rheophilic species Coreius guichenoti and Pelteobagrus vachelli. The transitional zones were dominated by Coreius heterodon and Rhinogobio cylindricus. The lacustrine zones were dominated by eurytopic species Hypophthalmichthys molitrix, Aristichthys nobilis, Hemiculter bleekeri and Cvprinus carpio. For the functional characteristics, fish assemblages in riverine and transitional zones were dominated by insectivorous species, equilibrium strategists and rheophilic species (e.g., Coreius heterodon and Coreius guichenoti). In lacustrine zones, the fish assemblage was dominated by habitat generalists common to lakes and reservoirs (e.g., Hemiculter bleekeri, Hypophthalmichthys molitrix, Aristichthys nobilis). Moreover, 18 exotic species (e.g., Protosalanx hyalocranius, Ictalurus punctatus, Megalobrama amblycephala, Tilapia) were collected in TGR, most of which only existed in the lacustrine zone. The results highlight the importance of freely flowing riverine reaches for conserving native fish in the upper Changjiang River and adaptive management strategies for fisheries in TGR.