• Shrub encroachment in alpine meadows on soil pH were examined. • Shrub encroachment changed soil porosity structure of in alpine meadow. • Shrub encroachment increased soil water and salt upward transport. • Shrub encroachment increased the potential risk of salinization. Alpine meadows are undergoing shrub encroachment due to climate change and human activities, which affects the health of alpine meadow ecosystems. Previous studies mostly focused on the impact of shrub encroachment on vegetation communities, but few studies were focused on the impact of shrub encroachment on soil pH. This study shed light on this topic by measuring soil moisture and water holding capacity under different levels of shrub encroachment (shrub coverage ranging from 8% to 90%) in alpine meadows located on the Qinghai-Tibet Plateau. Results showed that the intensification of shrub encroachment increased soil saturated water content, soil capillary moisture capacity and soil field capacity, but decreased soil moisture at the uppermost soil layer (0–10 cm). The increase of soil saturated water content and soil capillary moisture capacity increased soil pH. The intensification of shrub encroachment increased soil pH at soil depth of 0–10 cm, but decreased soil pH at soil depth of 20–30 cm. Overall, shrub encroachment could increase soil water and salt upward transport by reducing soil moisture and enhancing soil capillary moisture capacity, resulting in an increase of soil pH. These findings are conducive to better understand the impact of shrub encroachment on the redistribution of soil salinity in alpine meadows, and can provide a theoretical basis for predicting the changes of alpine meadow community facing future climatic change and human activities.