Habitat alteration often has important impacts on animal community and species diversity, but only a few studies have been conducted on how habitat desertification affects community composition of lizards at present. In this study, we investigated the differences in the community composition of lizards among three types of sampling fields with different stages of desertification using the line transect method in Jungar Banner and Dalad Banner in the Erdos region of Inner Mongolia, China. Subsequently, we explored their key influencing factors through canonical correspondence analysis (CCA). The results of our investigations showed that habitat desertification led to significant changes in the community composition of lizards. From the fixed and semi-fixed dunes to mobile dunes, the toad-headed lizard (Phrynocephalus frontalis) was the dominant species of the lizard communities, the multiocellated racerunner (Eremias multiocellata) showed gradual reduction in its population density, and the Mongolian racerunner (E. argus) disappeared in the semi-fixed and mobile dunes of severe desertification. With increasing habitat desertification in the three types of dunes, the population sizes and densities of different lizard species decreased gradually; the richness, Shannon-Weaver diversity index, and Pielou's evenness index of lizard species declined gradually; and the Simpson's dominance index increased significantly. These results indicated that desertification not only simplified the community composition of lizards, but also led to a decrease in lizard species diversity. Furthermore, desertification led to significant changes in the inhabited conditions of lizards. Significant differences were observed in vegetation height, proportion of Artemisia ordosica, bare ground and shelter percentages, and surface soil porosity and water content among the three sampling fields. The CCA results showed that these environmental factors were closely related to the changes in lizard community composition. In general, P. frontalis preferred the areas dominated by bare ground, while E. multiocellata preferred the region with sufficient shelter and loose moist soil. As for E. argus, this lizard species was frequently found in habitats with high vegetation.