Abstract: To understand the structure variation of fish assemblage of Hun River Basin in Liaoning Province of Northeast China, 46 sampling sites were investigated in 2010 and 2014. A total of 32 species and 15039 fish, belonging to 9 families and 6 orders, and 41 species and 10483 fish, belonging to 10 families and 6 orders, were identified in 2010 and 2014, respectively. The Mann-Whitney U test supported a significant increase in fish assemblage parameters like the number of fish species, Shannon-Wiener index, proportion of benthic species, proportion of herbivores individuals and proportion of carnivores individuals. Canonical correspondence analysis showed that in 2010, flow rate, conductivity, river rank and calcium ion were the primary environmental factors affecting fish assemblage, while in 2014, conductivity, river rank and ammonia significantly affect fish assemblage. The score of F-IBI were 48.7624.82 and 50.4117.35 in 2010 and 2014 respectively. By contrast in 2014, the health condition slightly increased and the sampling sites of very poor, poor, good and excellent decreased by 4, 1, 1 and 3 sites than those in 2010, respectively. Meanwhile, the sampling sites of moderate increased by 9 sites than those in 2010.