As the largest wetland nature reserve area for cranes and other large water birds in China, Zhalong National Nature Reserve plays an important role in maintaining regional ecological security. In 2011, composition structure of diatom communities were investigated during spring, summer and autumn. The biodiversity of diatom in this area are relatively high and totally 112 taxa(including 96 species, 16 varieties) were identified, belonging to 2 classes, 6 orders, 9 families and 32 genera. The diatom communities were analyzed by principal component analysis and cluster analysis was employed to analysis the relationship between diatom and environmental parameters. It showed that conductivity, total phosphorus and total nitrogen have great influence on the diatom distribution. Through the analysis, species preferring to alkaline and semi-alkaline habitat were identified, such as Navicula radiosa Kütz., Epithemia adnata, Fragilaria ulna var. acus(Kütz.) Lange-Bertalot. Due to the effect of land salinization, the water was affected by the alkaline and sort of salty weakly.Combined with the physical and chemical indicators of the water, we conclude that the water quality in Zhalong National Nature Reserve have been polluted slightly.