Located along the northeastern edge of the Qinghai‐Tibet Plateau in China, the Qilian Mountains are an important ecological barrier in Northwest China. Therefore, it is of great significance to study the plant water sources in subalpine habitats for understanding the ecological and hydrological processes in the Qilian Mountains. Here, based on the samples of precipitation, xylem water, soil water, river water, and spring water collected during May–October 2019 from subalpine habitats on the northern slope of the Qilian Mountains and the measured hydrogen and oxygen stable isotope values (δ2H and δ18O, respectively), the present study gained further insight into plant water sources in this region using the IsoSource model. Water absorption characteristics of shrubs were similar in subalpine habitats. Specifically, plants absorbed water primarily from the topsoil layer (0–30 cm) and rarely from the deep soil layers. Nevertheless, in the dry and growing seasons with high water demand, subalpine shrubs competed for water resources at similar depths. As a result of this competition, the utilization rate of deep soil water improved in some shrubs, expanding the differences in water sources of subalpine shrubs within the same habitat. In addition, in the dry and growing seasons, the water sources of the same subalpine shrub varied across different habitats. Compared with other subalpine shrubs, Salix cupularis Rehder, Salix oritrepha Schneid., Potentilla fruticosa L., Salix sclerophylla Anderss., Rhododendron anthopogonoides Maxim., and Rhododendron przewalskii Maxim. could alter their water use strategies with variations in water conditions, exhibiting a greater drought tolerance. These findings provide valuable information for understanding the subalpine region's eco‐hydrological processes and contribute to the selection of suitable species for the restoration of the subalpine ecological environment under the background of global change.