Alpine grassland desertification is a serious threat to the ecological security of the Tibetan Plateau. Studying the variations in soil carbon, nitrogen and microorganisms during desertification processes is helpful to reveal the biological mechanism driving the desertification of alpine grassland. In this study, the variations of soil carbon and nitrogen, enzyme activity, and bacterial community diversity under the conditions of non-desertification, light desertification, medium desertification and heavy desertification were analyzed. The results showed that the medium and heavy desertification decreased soil organic carbon, dissolved organic carbon, microbial biomass carbon, total nitrogen, soluble total nitrogen, soluble organic nitrogen, microbial biomass nitrogen, nitrate nitrogen and ammonium nitrogen; while light desertification had no significant impacts on soil organic carbon, microbial biomass nitrogen, nitrate nitrogen and ammonium nitrogen. The β-D-Glucosidase, Sucrase, Chitinase, Urease and Peroxidase activities decreased with the increasing desertification, and the most drastic decline occurred at the stage from light to medium desertification. Soil bacterial diversity increased under light desertification, and then decreased under medium and heavy desertification, but there was no significant difference in soil bacterial community structure under different degrees of desertification. RDA showed that there was a significant positive correlation between soil enzyme activity and bacterial diversity. PCA showed that soil organic carbon, microbial biomass nitrogen, peroxidase, and chitinase had great impact on dominant bacteria species. Therefore, the protection measures taken at the light desertification stage could effectively prevent soil attributes from becoming a more severe condition in alpine grassland, in addition, the role of key bacterial communities also should be concerned during the restore process of desertificated soil.