Based on soil samples at six habitats of Berberis vernae in different altitudes range from 2 300 m to 4 000 m in eastern of QinghaiTibet Plateau, we analyzed soil microbial community structure and diversity by highthroughput sequencing method. The results showed that: (1) in the soil of B. vernae habitats, the bacterial community mainly included 21 bacterial genera of 10 bacterial phylum, and the fungal community was made of 59 fungal genera of 8 fungal phylum such as Ascomycota and Basidiomycota. (2) The richness and diversity of bacterial community in 0-20 cm soil layer of Haidong Ledu No.1 site (hdld1) at low altitude was the highest, the richness of fungal community in 0-20 cm soil layer of Huangnan Zeku site (hnzk) was the highest, and the diversity of fungal community in 0-20 cm soil layer of Xining Datong site (xndt) was the highest. With the increase of altitude, the richness and diversity of bacterial community in 0-20 cm and 40-60 cm soil layers decreased firstly, then increased and then decreased, the richness and diversity of bacterial community in 20-40 cm soil layer showed a trend of increased firstly and then decreased, while the richness of microbial fungi community in 0-20 cm and 20-40 cm soil layers increased first, then decreased and then increased. The diversity of fungal community in 0-20 cm and 40-60 cm soil layers increased firstly and then decreased with the elevation, but the change trend of fungal richness in 40-60 cm soil layer and fungal diversity in 20-40 cm soil layer was not obvious. (3) Nitrate nitrogen (N), available phosphorus (OP) and available potassium (AK) had obvious effects on soil microbial community. Above all, the diversity of soil microbial community in B. vernae habitats at different altitude gradients in alpine regions showed a different trend as altitude change, which was mainly affected by environmental conditions, soil physical and chemical properties and vegetation distribution.