Variation patterns in gut microbial diversity among host species and populations offer valuable insights into the mechanisms underlying environment-host-microbiome interactions. However, the extent to which host phylogeny and geography drive these variation patterns in animal gut microbiota remains an open question. Amphibians and reptiles are important models to address this issue. Using 194 gut microbial samples of three amphibian and four reptile species inhabiting the Tarim Desert, we demonstrated phylosymbiosis in these animals, which was associated with heterogeneous selection and dispersal limitation. In interpopulation comparisons, Bufotes pewzowi and Teratoscincus przewalskii exhibited geography-dependent variations in their gut microbiota, particularly in relation to longitude and annual precipitation. These geographical patterns were linked to the heterogeneous selection of microbiota. Interestingly, the microbiota of B. pewzowi and T. przewalskii showed parallel variations with longitude, suggesting common selective pressures on amphibian and reptile microbiota. Finally, we found host genetic background did not account for the geographical pattern in their gut microbiota, even though it was also associated with geographical factors. This suggested environment-microbe interaction as a potential and independent ecological pathway mediating the associations between the environment and animals. Overall, these findings extend our understanding of variation patterns in gut microbiota and shed light on the underlying mechanisms.