In order to explore the characteristics of hydrogen-oxygen isotopes and ecological hydrological processes in different water bodies in the subalpine zone of Qilian Mountains, China, precipitation, soil water, plant water, groundwater and river water samples were collected from the subalpine of the Eastern of Qilian Mountains section from July to August in 2015. Qualitative analysis was used in hydrogen and oxygen isotope characteristics of different water bodies. Then, the mixing model of MixSIAR based on Bayesian theory was used to quantify the water absorption depth of shrub plant and the proportion of water source replenishment between different water bodies. The purpose is to illustrate the water migration relationship between water bodies, thereby to clarify the ecological hydrological process in the subalpine shrub area of Eastern Qilian Mountains. Results indicate that: (1) The isotopic values of various water bodies in the study area are affected by changes in the amount of precipitation, but precipitation has a smaller impact on river water. (2) Soil water of 0~20 cm is affected easily by precipitation and evaporation, while soil water of 60~80 cm is affected strongly by groundwater. (3) The water content of shrub plant in study area is mainly derived from precipitation and soil water under 0~20 cm. (4) Although the direct influence on the values of δ¹⁸O in groundwater and river water by precipitation is not obvious and their variation ranges are small, there are different degrees of response to precipitation, and river water responds faster to precipitation than groundwater.