Global surface temperature is predicted to increase by at least 1.5 degrees C by the end of this century. However, the response of soil microbial communities to global warming is still poorly understood, especially in high-elevation grasslands. We therefore conducted an experiment on three types of alpine grasslands on the Qinghai-Tibet Plateau to study the effect of experimental warming on abundance and composition of soil microbial communities at 0-10 and 10-20 cm depths. Plots were passively warmed for 3 years using open-top chambers and compared to adjacent control plots at ambient temperature. Soil microbial communities were assessed using phospholipid fatty acid (PLFA) analysis. We found that 3 years of experimental warming consistently and significantly increased microbial biomass at the 0-10 cm soil depth of alpine swamp meadow (ASM) and alpine steppe (AS) grasslands, and at both the 0-10 and 10-20 cm soil depths of alpine meadow (AM) grasslands, due primarily to the changes in soil temperature, moisture, and plant coverage. Soil microbial community composition was also significantly affected by warming at the 0-10 cm soil depth of ASM and AM and at the 10-20 cm soil depth of AM. Warming significantly decreased the ratio of fungi to bacteria and thus induced a community shift towards bacteria at the 0-10 cm soil depth of ASM and AM. While the ratio of arbuscular mycorrhizal fungi to saprotrophic fungi (AMF/SF) was significantly decreased by warming at the 0-10 cm soil depth of ASM, it was increased at the 0-10 cm soil depth of AM. These results indicate that warming had a strong influence on soil microbial communities in the studied high-elevation grasslands and that the effect was dependent on grassland type.