The Yangtze River is a biodiversity hotspot, and it has the most diverse fish assemblages on Earth. Dam construction is one of the main causes of fish biodiversity decline. The Three Gorges Dam (TGD) is the world’s largest hydroelectric dam, which is a cause of concern for ecologists worldwide, mainly regarding the negative impacts on biodiversity and the ecological processes in the region. Information on the biodiversity patterns of fish is vital for informing conservation and management strategies. However, few studies have articulated the principal mechanisms underlying the interactions between the biodiversity patterns of fish and anthropogenic habitat alterations after the TGD construction in the Yangtze River Basin. Here, we aimed to analyze the changes in the biodiversity patterns of the fish in the historical and current periods and to explore the effects of geographical and climate characteristics on the biodiversity patterns. The results showed that the fish species diversity in the current period has experienced a significant decrease. An average of 45.3 native species and 19.3 endemic species have been extirpated in the Yangtze River Basin. A total of 113 fish species have been classified as Critically Endangered (22), Endangered (39), Vulnerable (29) and Near Threatened (23). In addition, the alpha and gamma diversity have also decreased significantly. The analysis of the beta diversity showed a significant trend towards taxonomic homogenization. We found significant effects of geographical distance, temperature, precipitation and altitude on the beta diversity. This study will provide important information for the conservation and management of fish biodiversity in the Yangtze River Basin and other areas.