Oxytropis glacialis is one of the main poisonous weeds in the alpine grassland and desert grassland of the Qinghai-Tibet Plateau (QTP). It has a serious impact on the grassland degradation and the development of animal husbandry in the QTP. In this paper, the bacterial 16S rRNA in the root system soil of Oxytropis glacialis was sequenced by high-throughput sequencing and analyzed by bioinformatics methods. Combining with the physical and chemical properties of soil samples, the bacterial diversity and its relationship with soil physical and chemical factors was analyzed. The possible influence on root system soil bacteria of Oxytropis glacialis to form dominant species in alpine ecosystem was discussed. The results showed that the diversity of root system soil bacteria of Oxytropis glacialis was rich in different ecological environments, and was most affected by soil pH and organic matter. Meanwhile, the stable core microbiota network could be maintained, which could promote the formation of Oxytropis glacialis becoming dominant species in the alpine ecosystem.