Soil nutrients are ubiquitously heterogeneously distributed and such heterogeneity can greatly influence plant and population growth, interspecific competition and community structure and productivity. Despite these impacts, it is still unknown how soil nutrient heterogeneity affects community stability. We conducted a three-year experiment in an alpine meadow on the Qinghai-Tibetan Plateau, involving one homogeneous and six heterogeneous treatments of N, P, and K addition. The heterogeneous treatments varied in patch size, patch contrast, and number of patch types. Community stability in the homogeneous treatment tended to be the highest, likely due to high asynchrony among functional groups. However, such effects varied with patch size, patch contrast and number of patch types. Also, the effects of patch contrast and number of patch types on community stability and asynchrony among functional groups depended on patch size. The grass proportion was significantly affected by soil nutrient heterogeneity, and greater number of patch types increased the grass proportion at the small patch size, but not at the large one. Additionally, species richness, Shannon-Weiner index and Simpson index were greater in high patch contrast compared to the homogeneous treatment, but community evenness was not. These results suggest that soil nutrient heterogeneity can influence community stability by modifying functional group asynchrony and community evenness, rather than biomass proportions or other plant diversity indices. Our findings highlight the importance of incorporating soil nutrient heterogeneity in modeling the responses of alpine ecosystems to continuous nitrogen deposition and climate warming.