Seasonal dietary shifts of animals are important ecological adaptation strategies. An increasing number of studies have shown that seasonal dietary shifts can influence or even determine the composition of gut microbiota. The turpan wonder gecko Teratoscincus roborowskii lives in extreme desert environments, which have flexible dietary shift to fruit-eating in warm seasons. But the impact of such shifts on gut microbiota is poorly understood. Here, 16SrRNA sequencing and LC-MS metabolomics we used to examine the changes of gut microbiota composition and metabolic pattern of T. roborowskii. The results demonstrated that the gut microbes of T. roborowskii had significant seasonal changes, the diversity and abundance of gut microbiota in autumn were higher than those of in spring. Firmicutes, Bacteroidetes and Proteobacteria were the core gut microbes of T. roborowskii. Verrucomicrobia and Proteobacteria exhibit dynamic pattern of ebb and flow between spring and autumn.The composition and structure of gut microbes in different seasons perform specific metabolic functions, and this change may be an important adaptation for T. roborowskii to cope with dietary shifts and improve energy acquisition. Our study will provide a theoretical basis for exploring the adaptive evolution to special frugivorous behavior of the T. roborowskii, which is an important supplement to the study of the gut microbiology of desert lizards.