Soil fauna plays an important role in nutrient cycling and energy flow, and is also an important driver of ecosystem succession. The Qinghai-Tibetan Plateau, with an area of 2.5 million square kilometers, and elevation of over 4,500 meters, has been called "the third polar area of the earth". The wetlands of the Qinghai-Tibetan Plateau are an important biodiversity area. The Zoigê Wetland, located on the eastern Qinghai-Tibetan Plateau, is a typical example of an alpine meadow. Since the 1950s, the Zoigê Wetland has degraded as a result of global change and human activity, and parts have become desert-like with little plant coverage. The effect of this degradation on the structure and diversity of the below-ground soil biota is unknown. To investigate the effects of degradation on the soil meso- and microfauna in Zoigê Alpine Meadow, three degradation stages (marsh meadow, grassland meadow and sand meadow) were selected, and examined in July and October, 2008. A total of 9,450 individuals were captured from the soil meso- and microfauna, and classified into 4 phyla, 5 classes, 12 orders, 70 families and 104 taxa. The community was found to be dominated by nematodes, accounting for 85.79% of the individuals. Other common taxonomic groups were Arachnida (8.73%), Collembola (3.24%), Oligochaeta (1.32%), and insects (0.88%). In both July and October, abundance, richness and diversity in soil meso- and microfaunal communities were observed to be significantly less (P<0.01 and P<0.05) for each degradation stage. Differences among the three degradation stages were more significant in October. No significant changes were recorded in the Shannon diversity index, Pielou's index, and Simpson's diversity index (P>0.05). Percentages in each taxonomic group varied, without an obvious trend. The sand meadow had a greater relative abundance of Arachnida to Collembola than did the marsh meadow or the grassland meadow. The Sorensen similarity index showed a decline as degradation progressed, but this was not observed with the Morisita-Horn similarity index. Degradation thus had a greater influence on composition of the soil meso- and microfaunal community than on individuals belonging to dominant taxonomic groups. Diversity was higher in October than in July, as indicated by the higher values obtained for the taxonomic groups, diversity index, Sorenson similarity index and Morisita-Horn similarity index. This suggested that seasonal change can influence the structure and composition of the soil community. Furthermore, seasonal similarities between the three meadow stages, as shown by the Sorenson and Morisita-Horn indices, indicated that seasonal changes have a greater effect on taxonomic composition in the sand meadow than in the grassland meadow. The opposite pattern was observed for the abundance of dominant taxonomic groups. A greater number of individuals and taxonomic groups were found in the surface layer of the soil as degradation increased. Serious degradation of alpine meadows can significantly reduce taxonomic diversity and structural complexity within these meso- and microfaunal soil communities. Clearly this influences the ecological functions of alpine meadows.