Taking a typical river of northwest arid region such as Heihe river for example, through field surveys of aquatic ecosystems, aquatic organisms identification and data processing,the paper analyzed the feature of aquatic ecosystems spatial heterogeneity in Heihe river basin. Meanwhile,it identified and analyzed the major environmental factors of aquatic ecosystems spatial heterogeneity in the basin by use of the methods of correlation analysis and principal component analysis.The analysis showed that among every environment factor which impacts the aquatic ecosystems in Heihe river basin, there are some information redundant and interaction relationship.The absolute elevation has a good positive correlation relationship with the factors such as relative elevation, runoff depth, precipitation and net primary productivity(NPP), and has more obvious negative correlation relationship with evaporation, average temperature and drought index. The three indicators such as altitude elevation in terrain factor (DEM), rainfall and drought index in climatic factors have greater relationship with the feature of spatial distribution of aquatic ecosystem heterogeneity in Heihe river basin,which are the main factors of environmental effect to spatial heterogeneity of aquatic ecosystems in arid area of Heihe river basin.