Studying the interrelation of soil water and plant water is essential for an in-depth understanding of eco-hydrological processes. However, water use relationships and comparative studies between shrubs and alpine grassland of the northern Qinghai-Tibet Plateau remain poorly understood. In this study, we compared δ18O and δ2H values of water from soil, plant, precipitation, and groundwater between P. fruticosa shrub and alpine grassland locations at two neighboring sites in order to better understand the interface between plant and surrounding soils of shrubs and grasslands in the northern Qinghai-Tibet Plateau. Our results showed that δ18O and δ2H of soil water, precipitation, and plant water varied significantly over time and water sources in P. fruticosa shrub and alpine grassland sites. Both soil evaporation and plant transpiration at the P. fruticosa shrub site were relatively lower than they were at the alpine grassland site. Alpine grassland plant water had a stronger dynamic fractionation effect in the process of transportation and was more sensitive to environmental conditions. However, plants at the P. fruticosa shrub site displayed more flexible water use patterns, shifted their water sources between shallow soil water and deep soil water. Shrubs from alpine grassland leaded to changes in grassland water use, thereby changing soil water storage. The results of this study will provide theoretical basis for improving the availability and sustainability of soil water, provide guidance for meadow management from ecohydrological processes on the northern Qinghai-Tibet Plateau.