The Qinghai–Tibet Plateau (QTP) has an important function in ensuring the water ecological security of China, even Asia, and the soil water storage of alpine grassland is an important part of the ecosystem water. Grassland degradation directly affects the soil water storage capacity. However, the impact of degradation on specific soil storage capacity, especially alpine shrubs, is rarely studied. Here, we chose two plots of alpine non-degraded shrub and degraded shrub, using the automatic soil moisture monitoring system to study the change process of soil moisture storage, and then adopted the boosted regression tree (BRT) model to quantitatively evaluate the relative influence of environmental variables on soil water storage. Our results show: (1) The soil water storage in the growing season (May–September) is higher than that in the non-growing season (January–April and October–December), and the soil water storage reaches its highest in mid-July. (2) During the growing season, the 100 cm soil temperature was the most important factor affecting the seasonal variation in soil water storage, accounting for 51% of the total variation. During the non-growing season, the 40 cm soil temperature was the most important factor affecting the variation in soil water storage, accounting for 80% of the total variation. (3) The soil water storage of non-degraded Potentilla fruticosa shrub meadow increased by 6–25%, compared with degraded grassland shrub meadow during growing-season. (4) Various meteorological factors have a weak impact on soil water storage.