Microorganisms have important ecological functions in ecosystems. Studying the soil prokaryotic community composition of an alpine meadow in the Qinghai-Tibet Plateau and its key influencing factors would provide valuable information for revealing the special microbial flora of a unique geographical environment, and be useful for predicting global climate changes. In this study, the soil prokaryotic community compositions of an alpine swamp meadow and alpine meadow in the Qinghai-Tibet Plateau were analyzed using an Illumina Miseq high-throughput sequencing technique. A total of 23145 prokaryotic OTUs were detected, phylogenetically derived from 2 archaeal and 33 known bacterial phyla. Soil advantage categories included Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes, accounting for > 79% of the all phyla in the two meadow types. The prokaryotic diversity was higher in the alpine meadow than in the alpine swamp meadow. The two meadow types had significantly different soil prokaryotic community characteristics (P < 0.001). Based on a molecular ecological network analysis, we found that the alpine meadow network had a longer average path distance and modularity than the alpine swamp meadow network, making it more resilient to environment changes with a higher stability in response to climate change. The results of the Canonical Correspondence Analysis (CCA) and molecular ecological network analysis showed that soil pH was the main factor affecting soil prokaryotic community structure. In conclusion, the composition of the soil microbial community is an important indicator for evaluating environmental responses to global climate change. Soil prokaryotic community characteristics have significant differences in different alpine meadow soils. Understanding the variation and influencing factors could provide a theoretical basis for adaptive management and response to climate change in alpine meadow ecosystems.