Understanding the response of vegetation to a changing global climate is important. The relationships among 33 topographic, soil and climatic variables and 74 vegetation assemblages were analyzed by detrended canonical correspondence analysis (DCCA) to determine the most important variables that affect vegetation patterns and their distribution in different reaches of the Heihe River Basin. Altitude was the most significant factor across the entire basin and in the middle reach (oasis-desert area, 1289–3920 m). Mean temperature of the warmest month and mean annual evapotranspiration were the most significant factors in the upper reach (mountain area, 2180–547 m) and the lower reach (desert area, 820–2593 m), respectively. The annual average insolation and the aridity index also had significant relationships with vegetation distribution in the mountain area. Mean temperature of the coldest month and annual cumulated temperatures ≥ 10°C also were important in the oasis-desert area, and soil organic matter and groundwater depth in the desert area. Conservation of varying tree, shrub and grass species should be considered based on their thermal and water requirements in the mountain area.