Abstract: The microbiota plays a critical role in amphibian health, however, the exact impact of disease on the host microbiota assembly remains unclear, and microbiota-based health assessment and disease prediction is a promising yet poorly established field. Chinese spiny frog (Quasipaa spinosa) is an important “famous, high-quality and new” cultured amphibian in China, but diseases have become a major bottleneck restricting the development of breeding industry, especially during the initial stages of complete metamorphosis. Disruption of homeostasis or failure to reconstruct the skin microbiota leads to a variety of diseases. In this study, Illumina high-throughput sequencing technology was utilized to systemically explore potential associations between host health status (healthy spiny frogs (CTL), dysplastic disease (DD), and torticollis disease (TD)) and the composition, diversity and function of the skin microbiota. A total of 2997 amplicon sequence variants (ASVs) were obtained by sequencing, quality control and clustering, annotating 32 phyla, 76 orders, 167 orders, 259 families and 402 genera. Proteobacteria, Firmicutes and Bacteroidota were the dominant phyla (>1%) shared by all groups, but their abundance was significantly modified by health status of the host. At the genus level, 50 sensitive taxa were screened with 23 (e.g., Lactobacillus, Devosia, Shewanella and Luteolibacter) exhibiting high relative abundance in the CTL group, indicating the health status of spiny frogs. 19 taxa (e.g., Empedobacter, Bacillus and Brevinema) showed high relative abundance in the DD group, indicating dysplasia in spiny frogs, and 8 taxa (e.g., Elizabethkingia, Citrobacter and Acinetobacter) had high relative abundance in the TD group, indicating torticollis. Alpha diversity analyses indicated that the TD group had significantly lower diversity and evenness compared to the CTL and DD groups, and the microbiota composition also exhibited distinct separation. Functional predictions indicated significant differences between the CTL and diseased groups, which were mainly enriched in metabolism-relevant pathways. In summary, this study depicts the composition and changes in the skin microbiota of spiny frogs under different health conditions, highlighting the potential application of symbiotic microbiota modification in healthy amphibian culture and disease prevention.