【Objective】 With global climate change and overgrazing, shrub encroachment is extensively occurring in global grasslands. However, relatively little is known about how the structure of bacterial communities shifts with shrub encroachment. Thus, considering the aboveground plant community, soil carbon chemical composition, soil bacterial community structure and network beneath the canopies of three typical shrub species (Potentilla fruticosa, Spiraea alpina, and Caragana microphylla) as well as in adjacent grassland (as a control), the effects of shrub encroachment on the structure of soil bacterial communities and soil carbon pools were explored.【Method】 16S rRNA gene sequencing was used to investigate the bacterial communities and co-occurrence features among bacterial taxa while Fourier transform infrared spectroscopy (FTIR) was conducted to assess the soil organic carbon (SOC) chemical composition.【Result】 Shrub encroached grasslands (Potentilla fruticosa and Caragana microphylla) showed significant changes in aboveground plant community composition (P < 0.01) while the aboveground plant community diversity and richness remained constant (P > 0.05). The biomass of the three shrub plots was significantly higher than that of grassland (P < 0.05) whereas underground biomass showed no significant difference (P > 0.05). Shrub encroachment had no significant effects on SOC and total nitrogen (TN) contents, but weakened the differences of SOC contents between top- and subsoils, as shown by significantly higher SOC contents in the topsoil of the grassland than in its subsoil (P < 0.05), with no such trend in the three shrub plots.The SOC chemical composition in both top- and subsoils of the three shrublands and grassland was dominated by aromatics(except for deep soil in Caragana microphylla plots), with no significant difference in aromatic content between shrub and grassland plots (P > 0.05). However, the Caragana microphylla plots exhibited a surface-aggregated distribution of aromatics (P < 0.05). Random forest model analysis revealed that the distribution of Acidobacteria and Actinobacteria was the most important predictor of shrub encroachment in top and subsoils (P < 0.01). According to Non-metric multidimensional scaling (NMDS) analysis, the bacterial community composition of alpine grassland was significantly altered by shrub encroachment. Moreover, plant community composition and SOC chemical compositions were the main explanatory factors affecting bacteria community composition in both depths. Functional prediction analysis identified four biological metabolic pathways, including cellular processes, environmental information processing, metabolism, and genetic information processing, with metabolism being enriched in shrub plots (P < 0.05). Based on topological parameters of total links, complexity, and natural connectivity, the results showed that the soil bacterial network of shrublands was more complicated and stabilized than that in grasslands, and mutualism or commensalism may play an important role in establishing the bacterial community structure. 【Conclusion】 In summary, the results of this study suggest that shrub encroachment had an important regulatory effect on soil bacterial community structure and soil carbon pool. The results enrich the literature on soil microbial community in alpine grassland and provide a theoretical basis for the effect of soil carbon source and sink in alpine grassland.