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Persistent global warming exacerbates the occurrence of extreme high-temperature events, exerting destructive impacts on numerous organisms including amphibians. While it has been well-established that temperature can significantly influence the structure and function of gut microbiota, little research has addressed whether and how high temperature impact the initial colonization of gut microbiota during the embryonic stage of amphibians. In this study, 16S rRNA technology was employed to detect the diversity and composition of gut microbiota in Bufo gargarizans embryos developing in the high temperature group (HT) and the control group (Con). Additionally, effects of high temperature on embryonic growth and development were also investigated. Results indicated that elevated temperature significantly accelerated embryonic development, especially during the organogenesis stage. Lower hatching rate, higher malformation rate and greater embryo body mass were observed in the HT group versus Con group. Crucially, exposure to high temperature impaired gut microbial colonization and altered microbial profile, characterized by lower α diversity, reduced relative abundance of beneficial bacteria (e.g., Bdellovibrionota and Myxococcota), and elevated relative abundance of pathogenic bacteria (e.g., Fusobacteriota, Microbacteriaceae, and Shewanella) in the HT group. This study provides valuable insights for assessing the detrimental impacts of global warming on the gut microbial colonization of amphibians.