[Objective] Permafrost stores massive amounts of organic carbon, accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the organic carbon stored in permafrost acts as the positive feedbacks to aggravate the global greenhouse effect. In this study, to understand the distribution and diversity of microbes in the permafrost, the microbial compositions along a stratigraphic permafrost soil profile were studied from the Qinghai-Tibetan Plateau. [Methods] The molecular biology methods were used to amplify the archaeal and bacterial 16S rRNA genes and the fungal ITS sequences, and then constructed their gene clone libraries, respectively. Phylogenetic analyses of the sequences based on those sequence similarity were carried out and the community diversity index was calculated. [Results] Phylogenic analysis of the archaeal 16S rRNA gene clone library revealed that all the archaeal sequences were affiliated to two phyla, Crenarchaeota and Euryarchaeota, which comprise 29.0% and 71.0% of the total clone sequences, respectively; Crenarchaeota was classified into only one lineage, Group1.3b/MCG-A, which accounted for 29.0% of archaeal clone sequences, and Euryarchaeota was classified into four lineages, of which methanomicrobiales (52.0%) was the predominant group in the phylum of Euryarchaeota. In the active layer of permafrost, Group1.3b/MCG-A、Methanomicrobiales and Methanosaetaceae were the predominant groups in the archaeal clore sequences; In the transition layer, The predominant groups belong to Group1.3b/MCG-A and Methanomicrobiales; In the permafrost layer, Methanomicrobiales was the only predominant lineage. The retrieved bacterial 16S rRNA gene sequences were classified into ten lineages, of which Actinobacteria, Firmicutes and Proteobacteria were the predominant groups, accounting for 28.9%, 16.9% and 12.1% of bacterial clone sequences, respectively. In the active layer, the predominant groups of bacterial belong to Proteobacteria and Firmicutes, the transition layer and the permafrost layer are relatively similar on bacterial composition, the predominant groups of bacterial were affiliated to Actinobacteria. All the fungal ITS sequences were affiliated to two phyla, Ascomycota and Basidiomycota, which comprise 75.3% and 24.7% of the total ITS sequences, respectively. Cladosporium sp. and Pseudeurotium bakeri were the predominant lineages affiliated to Ascomycota, while Dioszegia sp. was the predominant lineage affiliated to Basidiomycota, accounting for 35.5%, 34.4% and 22.6% of fungal ITS sequences, respectively. In the active layer of permafrost, Pseudeurotium bakeri was the only predominant lineage in the fungal sequences. in the transition layer and the permafrost layer, the predominant groups belong to Dioszegia sp. and Cladosporium sp.. [Conclusion] The permafrost soil has high diversities of the archaeal, the bacterial and the fungal communities along the vertical soil profile. The microbial composition and distribution between the active layer and the permafrost layer were different significantly.