Amphibians have a unique life history and are extremely sensitive to habitat changes. They are important indicator groups for monitoring environmental quality changes and assessing ecosystem health. Amphibians have become the most threatened animal group in China due to habitat loss and degradation, environmental pollution, climate change, overharvesting, invasion of alien species, and biological internal factors. Strengthening of resource survey and population monitoring of amphibians constitutes the fundamental work for amphibian diversity protection and endangered species rescue. Traditional amphibian monitoring is mainly based on morphology and acoustics, which is time-consuming, laborious, and highly dependent on professional classification knowledge and investigation experience. Furthermore, it is difficult to find some rare species given their strong concealment. The investigation method based on environmental DNA (eDNA) has unique advantages. It is fast, sensitive, efficient, non-invasive, low cost, and independent of traditional classification experience, etc. This can make up for the shortcomings of the traditional investigation methods and provide a new tool for amphibian diversity monitoring and protection. eDNA has been successfully applied in amphibian research, such as monitoring alien invasive species, rare and endangered species protection, biodiversity assessment, and species abundance or biomass estimation. However, in practical application research, due to different application environments, target organisms, sampling protocols, and primer selection, the experiment results were extremely varied. Although previous studies have promoted the progress of this technology, they could not provide systematic guidance for amphibian investigation and monitoring, and there is still uncertainty in the complex ecological processes of eDNA from amphibians. In this review, we summarized the application of eDNA in amphibian monitoring. We analyzed the critical factors that should be considered in its application, including the shedding and capture of eDNA, the selection of sampling location and time, the transport and deposition of eDNA, and the degradation of eDNA, as well as the associated biotic and abiotic factors. In addition, we discussed the limitations of the application of eDNA and provided several optimization suggestions for improving the efficiency and accuracy of the amphibian monitoring base on eDNA. Finally, we looked toward future research directions to fully exploit the application potential of eDNA in amphibian monitoring and provide new ideas for amphibian diversity protection and management.