Alpine forest soil is one of the most fragile terrestrial carbon pools, faces heightened vulnerability as a result of global climate warming. The intricate freeze-thaw pattern, influenced by rising temperatures, is expected to undergo modifications, consequently impacting the structure of soil microbial communities and disrupting essential soil microecological processes. To gain insights into these dynamics, this study employed 16S rRNA sequencing technology to examine the response of microbial community structure and diversity to seasonal freeze-thaw in soils at different elevations of Mount Segrila in Tibet. The findings of this study reveal that the occurrence of freeze-thaw events did not induce significant shifts in the dominant bacterial and fungal groups at the phylum level. The prevailing bacterial groups identified were Proteobacteria, Actinobacteriota, and Acidobacteria, while the dominant fungal phyla were Basidiomycota and Ascomycota. At the genus level, notable variations were observed in the microbial community structure and composition before and after freeze-thaw events. Interestingly, bacterial communities exhibited greater susceptibility to freeze-thaw, while the fungal community displayed a heightened sensitivity to changes in elevation. Furthermore, this study explored the impact of freeze-thaw events on the alpha-diversity of microbial communities at different elevations. At the operational taxonomic units level, the results indicated a significant increase in bacterial community diversity across all elevations, as well as in the fungal community at elevations of 3500 m and 4300 m. The increase in diversity was primarily influenced by the clay and silt content within the soil matrix. Additionally, the study revealed that the differences in microbial community composition became more pronounced at varying elevations, with distinct driving factors identified before and after freeze-thaw events. Prior to freeze-thaw, factors such as C/N, available potassium, CO₃^2-, soil moisture, clay and silt content played significant roles in shaping the microbial community. Conversely, after freeze-thaw events, pH and available phosphorus emerged as the main influencing factors. Compared with bacteria, the influence factors of fungal community structure were more different between elevations. The comprehensive understanding gained from this study on the response of soil microorganisms to freeze-thaw events in alpine forests at different elevations holds profound implications. As the threat of climate change looms, comprehending the intricate relationships between environmental factors and microbial communities becomes increasingly imperative to predict and mitigate the potential consequences on ecosystem stability. This study provides an important basis for further understanding the response of soil microorganisms to freeze-thaw in alpine forests at different elevations under the background of climate warming.