The Qilian Mountains are an important ecological security barrier in the northwest China and a major water supply area for the Hexi Corridor. It is of great significance to study their hydrological processes. Based on the stable isotope values of precipitation, soil water and groundwater in the subalpine shrub zone of the eastern Qilian Mountains from May to October 2019, their stable isotope characteristics as well as the recharge and infiltration of soil water were analyzed by the lc-excess method and the lc-excess balance equation. The results showed that stable isotopes of precipitation showed significant enrichment in spring and depletion in summer and autumn, characterized by large fluctuations. Stable isotopes of soil water were enriched in summer and depleted in spring, appearing a tendency of gradual decrease with the increase of soil layer depth. However, stable isotopes of groundwater had the smallest fluctuations. Soil water was obviously recharged by precipitation in summer, but lower recharge was observed in spring and autumn. The main contributors to soil water recharge were precipitation events with the intensities of 10–20 mm/day and 20–30 mm/day. In subalpine shrub zone, both piston flow and preferential flow patterns coexisted in the infiltration of soil water, with a relative contribution rate of 76% from plug flow and 24% from preferential flow to groundwater recharge. The results are of theoretical value and practical significance for understanding hydrological processes and evaluating groundwater quantity in the subalpine shrub zone.