Soil microorganisms,an essential component of terrestrial ecosystems,play important roles in driving biogeochemical processes and maintaining ecosystem function. Studying soil microbial functional genes and their impact factors of alpine meadow in Qinghai-Tibet Plateau would help us understand the functional metabolic potential of soil microorganisms and provide valuable information for predicting the response of Qinghai-Tibet Plateau to global changes. Here,soil microbial functional genes in alpine swamp meadow and alpine meadow at Qinghai-Tibet Plateau were analyzed using a functional gene array technique (GeoChip 4.0). A total of 45818 functional genes were detected in two meadows,involving 16 key microbial-mediated biological processes. The results of Detrended Correspondence Analysis (DCA) and dissimilarity test showed significant differences in the microbial community structure between two types of meadow. All key carbon and nitrogen metabolism processes mediated by microorganisms were detected,among which, alpine swamp meadow had higher gene abundance and metabolic potential involved in carbon degradation and nitrogen cycling than alpine meadow,though soil organic carbon and total nitrogen contents of two types of meadow were relatively stable. The results of Canonical Correspondence Analysis (CCA) showed that soil pH and moisture were the main factors shaping the structure of microbial functional genes. In summary,our results will help us understand the impacts of environmental changes on the structure and function of alpine grasslands and provide scientific reference for their conservation and management.