Abstract: River ecosystem investigation is the basis for the recovery of impaired river ecosystem. Taking the Hun River Basin in Liaoning Province of Northeast China as study area, 62 sampling sites were investigated. A total of 34 species, belonging to 29 genera, 10 families and 7 orders, were identified. They were dominated by species of Cyprinidae and Cobitidae, and these two orders accounted for 88.5% and 6.7% of the total amount of fish captured, respectively. Three groups were distinguished by the cluster analysis according to the similarity of fish community structure. The first group is in the upstream of Hun River, dominated by Phoxinus lagowskii, Nemachilus toni, Cobitis granoei. The second group is in the tributaries of its midstream, with moderate tolerance species, such as Carassius auratus, Pseudorasbora parva, Zacco platypus as indicator species. The last group is in the mainstream and tributaries at its middle and lower reaches, and the indicator species of this group is Hemiculter leucisculus. The canonical correspondence analysis (CCA) showed that the altitude, river level, suspended solids (SS), percentage of forest area, percentage of farmland area, and total suspended solids (TDS) were the primary environmental factors affecting the fish community in the basin.