The spatial distribution pattern of aquatic organisms inriver is closely related to the environmental factors of river basins, while human activities significantly change the heterogeneity of river habitats, which changes the structure and function of river water ecosystems. Studying the key environmental factors affecting the distribution of plankton is the basis of river water environmental protection and water ecological conservation, and is of great significance for the conservation of aquatic ecosystems and the construction of regional ecological civilization.Taking the typical river, Heihe River in the arid region of Northwest China as an example, this paper studies the plankton biodiversity and spatial distribution characteristics of the river basin through the sampling survey and statistical analysis of river plankton in the Heihe River Basin; Spatial Correlation Analysis (CA) and Principal Component Analysis (PCA) methods were used to identify the environmental factors affecting the plankton in the basin, and Canonical Correlation Analysis (CCA) method was used to screen out the key impact factors affecting the distribution of plankton. Studies have shown that there are certain correlations between environmental factors affecting plankton in the Heihe River Basin.There is a good positive correlation among absolute elevation and relative elevation, precipitation, runoff depth, Net Primary Productivity (NPP), Normalized Difference Vegetation Index (NDVI), slope and exposure. There was a significant negative correlation among absolute elevation and temperature, evaporation and drought index. The correlation coefficients were-0.842,-0.890,-0.779 respectively. Through CCA analysis, the elevation, precipitation and drought index are closely related to the distribution pattern of plankton in the basin, and they are key factors affecting plankton in the basin.