Under the effect of microbial metabolic activities, the mineralization and decomposition of organic carbon and nitrogen compounds in the soil release mineral nutrients and carbon dioxide, which profoundly affects the circulation and transformation of soil C, N, and other elements in the natural ecosystem, the supply of soil nutrients and the renewal of organic matter, and is of great significance to the succession and distribution of aboveground vegetation. Combined with soil physicochemical analysis and High throughput quantitative PCR(quantitative microbial element cycling, QMEC) technology, this study investigated the content of soil organic C and total N, soil respiration rate, net N mineralization rate and the abundance of C and N mineralization genes, and further explored their correlation with vegetation, climate, and soil factors in alpine shrub soils across the Himalayan-Gangdise regions on the Tibetan Plateau. The results showed that there were significant differences in the content and mineralization rate of C and N elements, and the abundance of C and N mineralization genes in the soils of different shrub types. Among them, soil respiration rate, net N mineralization rate, soil organic C and total N content in the Rhododendron nivale and Juniperus pingii var. wilsonii shrub areas were significantly higher than those in the Caragana versicolor, Dasiphora fruticose, and Sophora moorcroftian shrub areas, but the abundance of C and N mineralization genes was on the reverse. Soil respiration rate, net N mineralization rate, soil organic C and total N content were positively correlated with the mean annual precipitation. However, the abundance of C and N mineralization genes was negatively correlated with the mean annual precipitation, but positively correlated with the soil pH. Meanwhile, pH was negatively correlated with the mean annual precipitation, humidity index, and soil water content. All these results indicated that precipitation could reduce soil base saturation and increase soil hydrogen saturation by increasing the leaching of base ion, causing soil acidification and affecting the process of C and N cycle, thus affecting the turnover of C and N elements and determining the storage of C and N elements in the soils of different shrub types. Further, a significantly positive correlation was observed between the abundance of C and N mineralization genes, suggesting the close coupling relationship between soil C and N cycling processes. These results provide important information and reference basis for the accurate assessment of soil C and N pools and their dynamic balance of storage on the Tibetan Plateau.