Soil water is a link between different water bodies. The study of soil water evaporation is of great significance to understand the regional hydrological process, promote environmental remediation in arid areas, and rationalize ecological water use. On the basis of soil water δ2H and δ18O data from April to October 2017 in the Xiying River basin in the upper reaches of the Qilian mountains, the lc-excess and Craig-Gordon model were applied to reflect the evaporating fractionation of soil water. The results show that the change in evaporation loss drives the enrichment of soil water isotopes. The signal of evaporative fractionation of soil water isotopes at different elevations has spatiotemporal heterogeneity. From the perspective of time dynamics, the evaporation loss of the whole region during the observation period was affected by temperature before July, while after July, it was controlled jointly by temperature and humidity, evaporation was weakened. Soil salt content and vegetation played an important role in evaporation loss. In terms of spatial dynamics, the soil moisture evaporation at the Xiying (2097 m) and Huajian (2390 m) stations in the foothills area is larger than that at the Nichan station (2721 m) on the hillside and Lenglong station (3637 m) on the mountain top. The surface soil water evaporation is strong, and the evaporation becomes weak with the increase of depth. The research has guiding significance for the restoration and protection of vegetation in arid areas and the formulation of reasonable animal husbandry policies.