This research has been undertaken to reveal the changes in the community structure of epilithic moss mites and the response of these mites to environmental factors under different grades of rocky desertification environment. In this study, epilithic moss mites were collected in a demonstration area for rocky desertification management in Bijie Salaxi, with the following rocky desertification grades as habitat gradients: without rocky desertification, potential rocky desertification, light rocky desertification, moderate rocky desertification, and severe rocky desertification. The differences in the number of individuals, taxa, diversity index, dominance index, richness index, evenness index, and the effects of environmental factors on moss mite communities were revealed by one-way ANOVA, correlation analysis, and redundancy analysis for different grades of these mites. The results show that a total of 11,563 epilithic moss mites were captured in the study area, belonging to three orders, 100 families, and 171 genera, with Nanorchestes and Trichogalumna as the dominant taxa. With the deepening of rocky desertification, the dominant number of Nanorchestes and Trichogalumna increased. Still, the percentage of very rare genera also decreased, and there were differences in the composition of the dominant genus taxa in different grades of rocky desertification. Different grades of rocky desertification habitats had significant effects on the diversity index and richness index of moss mite species but not on the number of taxa, individuals, dominance index, and evenness index. The overall epilithic moss mite communities in different habitats were moderately dissimilar. Air temperature and rock temperature had strong effects on each index of moss mite diversity, whereas light factors and air humidity had a weak impact on these indices. Amongst the communities, those of Scheloribates are more sensitive to rock temperature variation, while Blattisocius, Ledermuelleria and Camerobia correlate more with a light variation. Parholaspulus, Blattisocius, Camerobia, Haplochthonius, Gymnodamaeus, etc. were more sensitive to changes in air humidity. The research shows that there are differences in moss mite community structure under different rocky desertification grades, rocky desertification has caused some effects on moss mite community structure, and the use of mite dominant taxa genera can give preliminary indications of the rocky desertification environment; meanwhile, there is a specific correlation between mite taxa and habitat environment changes.