In order to understand the variations of soil faunal diversity under different natural alpine vegetations in West Sichuan, an investigation was made on the soil faunal communities under alpine coniferous forest, shrub, and meadow from August 2008 to June 2009. A total of 48343 individuals were collected, belonging to 7 phyla, 16 classes, 31 orders and 117 families. There was a great difference in the dominant groups of soil macro-fauna, and a significant difference (P < 0.05) in the number of soil faunal groups under different vegetations. Both the individual density and the group number of soil fauna decreased obviously with increasing soil depth, and were significantly higher (P < 0.01) in moss layer than in litter layer in coniferous forest. Significant difference (P < 0.01) was also observed in the density-group index among the three vegetations. The maximum biomass of soil macro-fauna was found in June. Jacard indices indicated that disturbed meadow had the lowest similarity of soil faunal community with the other vegetations. It was suggested that vegetation type had significant effects on the community structure of soil fauna, while aspect, altitude, and disturbance also had definite effects.