Distribution characteristics of fish assemblages and environmental variation in emerged plant, floating-leaved plant and blank habitats were studied. Emergent plant habitat supported the greatest fish biomass, density and body size, followed by floating-leaved plant habitat, and those of blank habitat was the lowest. Transparency of emergent plant habitat decreased during the period, but of blank habitat increased. Species number of dominant fish of emergent plant habitat compared to the others decreased from four species, i.e., Hemicculter leuciclus, Pseudobrama simoni, Carassius auratus and Ophicephalus argus in May to the single one, C. auratus in September. Those of blank habitat increased from two species, H. leuciclus and Pseudorasbora parva to four species, H. leuciclus, C. auratus, P. parva and O. argus. This result suggested that emergent plant with excessively high density could worsen habitat physical and chemical conditions, resulted in the fish’s emigration to unvegetated area. Those of floating-leaved plant habitat from two species, Cultrichthys erythropterus and P. simoni, changed into four species, C. erythropterus, P. simoni, H. leuciclus and P. parva. The increasing structure complexity and biomass of floating-leaved macrophyte promoted the increase of dominant fish species number with seasonal change. C. auratus, C. erythropterus and H. leuciclus displayed special preferences on emergent plant, floating-leaved plant and blank habitats respectively. Fish’s special habitat preference was determined by plant physical morphology, habitat characteristics and fish breeding habits.