Invertebrate fauna as the main soil fauna is one of the important biological factors affecting litter decomposition, which plays an essential role in maintaining material circulation and energy flow of terrestrial ecosystems. Alpine timberline ecotone is an important transition region of mountain vegetation vertical band with more habitat complexity and species diversity than the adjacent ecosystems. Temperature fluctuation and freeze-thaw cycle frequency in timberline was significantly higher than that in coniferous forest, in order to understand the environmental difference in timberline ecotone on the influence of invertebrate community structure and diversity in the process of litter decomposition, a field experiment using litterbag method was carried out at the end of two main periods (snow cover season and growing season), the invertebrate community structure and diversity was studied in the foliar litter of Salix cupularis, Rhododendron lapponicum and Sorbus rufopilosa, three representative shrubs in the alpine timberline ecotone. The results showed that the invertebrate community diversity and density of individual and groups varied with the altitude, seasons and litter species, and invertebrate diversity influenced by seasonal variation was more significant than the altitude and litter species. The interaction of three factors(altitude, seasons and litter species) affected not only the invertebrate community diversity and evenness, but also the individual density and group density. At the end of snow cover season, Shannon index H, Pielou index J and Margalef index D was highest in the coniferous forest, and Simpson index C was highest in the timberline, while group density and individual density at the end of growing season was significant higher than that of snow cover season. In general, invertebrate fauna was the most abundant at the end of growing season, and relatively rich in timberline than in coniferous forest. This means that with increasing of shrub density and litter input quantity, invertebrate diversity is likely to increase in the future climate change scenarios.