Fish assemblage will change along with the river habitat environment. In order to find the response degree of fish assemblage to fish culture within low-head-dam water, two low-head dams (including the upstream and downstream dams) of the Wulong River (a tributary of the lower reach of the Yangtze River, China) were selected as sampling sites, where the habitat variables, the fish diversity and fish assemblage structure were surveyed for 6 times from 2013 to 2014 in these wadeable reaches of the sampling sites. A total of 24 fish species which belong to 5 orders, 21 genera and 24 species were caught, with dominant Cyprinidae accounting for 58.3% of the total. After an analysis on the influences of temporal changes and local habitat conditions upon the fish assemblage, seasonal factors were found to have no apparent effect on the fish assemblage structure. The spatial location (the upstream dam or the downstream dam) affected the assemblage's structural differences significantly, which were determined by the abundance of Hemiculter leucisculus, Abbottina rivularis, Rhodeus sinensis, Acheilognathus macropterus in the upstream site, and the abundance of Gambusia affinis in downstream site. Besides, all the three habitat variables including dissolved oxygen, conductivity and current velocity exerted a great impact on the fish assemblage. The differences in habitat environment bring about some great influences on the fish assemblage, showing in the dramatic decrease of capture weight, quantity, density and diversity of fish in the sampling sites of the downstream dam, which are probably caused by the fish culture within the low-head dam.