Abstract: The examination of the impact of physical habitat characteristics on fish community structure remains limited. To elucidate this influence, 14 and 18 sampling sites were respectively designated during the dry and wet seasons in the Hulun Lake Basin in 2021 to gather fish data. Utilizing remote sensing technology, corresponding physical habitat characteristics, including fractal dimension (FD), water surface area (Area), and Digital Elevation Model (DEM) were derived. Cluster analysis and redundancy analysis (RDA) were employed to scrutinize the response of fish community structure and distribution to physical habitat factors in the Hulun Lake Basin. The results reveal that both physical habitat characteristics and fish communities could be classified into four groups, each exhibiting distinct spatial distribution characteristics. The average similarity of the two clustering groups in dry season and wet season was 41.29% and 63.06%, respectively. Habitat factors FD, Area, and DEM influenced fish community diversity in the Hulun Lake Basin, with Area and DEM exhibiting a greater impact than FD. Furthermore, different fish communities responded differently to habitat factors: dominant species Hemiculter bleekeri and Cultrichthys erythropterus showed a significant positive correlation with DEM, resident omnivores Rhodeus sericeus, Carassius auratus gibelio, and Phoxinus lagowskii were significantly positively correlated with Area, while carnivorous species Silurus asotus and Esox reicherti were significantly positively correlated with FD. This study offers valuable insights for the ecological restoration of fish in the Hulun Lake Basin, serving as a guide for the protection and restoration of fish in cold and arid inland lakes in the north.