To support the synergistic decision-making of ecological protection and hydropower development in the headwater region of the Dadu River, and to clarify the structural characteristics of fish communities, spatial pattern of fish diversity and their conservation value in this region, we systematically collected fish samples from 11 rivers in the headwater region of the Dadu River in 2024 and conducted a study on the structure and diversity of fish communities. The results showed that a total of 18 fish species were collected, belonging to 12 genera, 5 families and 3 orders, including 14 native species, 4 exotic species, and 9 rare, protected and endemic species. Schizopygopsis daduensis was the dominant species across the entire study area. NMDS analysis revealed that the fish communities in the two main trunk streams of the headwater region had obvious differentiation characteristics: the fish communities in various tributaries of the Chuosijia River basin showed high similarity, while those in the Zumuzu River basin had great differences. SIMPER indicated that Triplophysa stoliczkai and Aristichthys nobilis were the main contributing species driving community differentiation, with contribution rates of 29.96% and 10.99%, respectively. In terms of species diversity, a spatial distribution pattern of significantly higher diversity in trunk streams than in tributaries was presented, among which the Zumuzu River had the highest Margalef richness index (2.02) and Shannon diversity index (1.82). The random forest model analysis showed that the Shannon diversity index and Margalef richness index were mainly driven by topographic and hydrological factors, with altitude (5.29%) and river width (4.14%) as the key factors, while the Pielou evenness index was most significantly affected by dissolved oxygen (3.10%). This study clarified the composition of fish communities and the pattern of fish diversity in