In order to elucidate the distribution characteristics of soil microorganisms at different altitudes, we selected Sejila mountain as a model area, a typical forest ecological area in southeastern Tibet. In this study we investigated the cultivable microorganisms and the richness of fungal community composition and relative abundances along an altitude gradient (approximately 3 400~4 600 m) in Sejila mountain. The amount of soil cultivable microorganisms in the 0—5 and 5—10 cm layer showed the following rank order: bacteria＞actinomycetes＞fungi, and the number of fungi was significantly correlated with altitude, while the number of bacteria and actinomycetes had no obvious change with altitude. The high-throughput sequencing results showed that there were 4 phyla, 18 classes, 47 orders, 74 families, and 93 genera of fungi detected. Basidiomycota and Ascomycota were predominant fungal at the phylum level, and Agaricomycetes had the highest relative abundance at the classes level. Alpha diversity analysis showed that the soil fungal abundance and diversity of the Quercus aquifolioides forest in lower altitude and the alpine grassland in the higher altitude area were higher, while the Rhododendron aganiphum and Abies georgei var. smithii forest in the middle altitude (3 900~4 110 m) was lower. The redundancy analysis found that, at the phylum and class classification level, the fungal community was mainly caused by soil organic carbon and total nitrogen contents, while the influence of altitude was relatively small. The results suggest that the distribution of microorganisms at different elevations may mainly depend on soil properties and vegetation type.