Alpine shrublands in the Three Rivers Source Region (TRSR) store substantial soil total nitrogen (N); however, limited information is available regarding its storage and controlling factors. To quantify the storage and controlling factors of soil total N stock, we analysed 66 soil profiles from samples obtained from 22 shrubland sites located across the TRSR on the Tibetan Plateau. Analytical methods, such as ordinary least squares regression, one-way analysis of variance, curve estimation, and variation partitioning were used to evaluate the effects of soil characteristics (soil organic carbon), vegetation characteristics (community types and ground cover of shrublands), climatic factors (mean annual temperature - MAT), and topographical features (slope) on soil N stock. Our results showed that soil N storage at a soil depth interval of 0-100 cm was 63.10 ± 27.41 Tg (Tg = 1012 g), with an average soil N stock of 2.44 ± 1.06 kg m-2 in the TRSR shrublands. Although the type of vegetation community had a small effect on soil N stock, the latter increased with increasing shrubland ground cover and soil organic carbon. However, soil N stock decreased with increasing topographical slope and MAT. Furthermore, changes in MAT primarily affected the N stock of topsoil. Among all the controlling factors, soil organic carbon explained most of the variation in the soil N stock. Considering the effects of global warming, an increase in MAT has decreased the soil N stock. Long-term monitoring of changes in soil N stock should be conducted to improve the precise estimation of soil N storage across the shrublands in the TRSR of the Tibetan Plateau.