Wastewater treatment plants (WWTPs) in plateau regions have unique microbial community structures. In this study, Illumina high-throughput sequencing technology was applied to investigate microbial communities of plateau WWTPs. The research showed that microbial diversities and richness were negatively associated with the altitude and positively to the water temperature to a certain extent. The dominant phyla of plateau and control WWTPs were similar, which mainly included Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes. In plateau WWTPs, the LEfSe analysis found 4 biomarkers which can catabolize aromatic compounds, indicating the microorganisms that can degrade refractory organics might survive better in plateau WWTPs. The analysis of functional genera and enzymes showed that there was no significant difference in abundances of organic degrading bacteria, but the nitrogen removal bacteria were less abundant and phosphorus removal bacteria were more abundant in plateau WWTPs.