Abstract: To investigate the microbial diversity, nutritional properties of fresh camel milk and sour camel milk from Fuhai County, Altay Prefecture, Xinjiang, this study employed high-throughput sequencing technology to analyze the microbial community structure. PICRUSt2 software combined with the KEGG and MetaCyc databases was applied to predict gene functions, and multivariate statistical methods were employed to systematically characterize and compare the two types of samples in terms of physicochemical indices and nutritional composition. The results showed that the dominant bacterial phyla in both fresh camel milk and sour camel milk were Bacillota and Proteobacteria. The dominant fungal phylum changed from Ascomycota and Basidiomycota in fresh camel milk to Ascomycota in sour camel milk. Compared with fresh camel milk, the dominant bacterial genus in sour camel milk shifted from Lactococcus to Lactobacillus, and the relative abundances of genera such as Streptococcus and Pediococcus increased significantly (P<0.05). The dominant fungal genera shifted from genera such as Apiotrichum and Issatchenkia to genera including Kazachstania, Candida and Debaryomyces, accompanied by the inhibition of several potentially pathogenic genera. Gene function prediction revealed that the overall metabolic functions of bacterial and fungal communities in sour camel milk were significantly enhanced. Specifically, the predicted relative abundances of core functional genes-involved in amino acid metabolism and lipid metabolism in bacterial metabolic pathways, folding, sorting, and degradation in genetic information processing, and fungal TCA cycle II (plants and fungi)-were significantly higher than those in fresh camel milk (P<0.05). Physicochemical analysis showed that pH, titratable acidity, and lactose content were the key indicators distinguishing the two sample types. Nutritional analysis revealed that the total amino acid content and the proportion of essential amino acids in sour camel milk were significantly increased (P<0.05), and the flavor amino acid profile was optimized, with glutamic acid, leucine, and threonine identified as the key differential amino acids. At the same time, the relative contents and species diversity of functional components such as polyunsaturated fatty acids, branched-chain fatty acids, and odd-chain fatty acids increased significantly (P<0.05). Twenty-eight key differentially fatty acids were screened, and six fatty acid nutritional evaluation indices, including the thrombogenicity index and health-promoting index, were significantly optimized (P<0.05). In summary, traditional fermentation coordinately enhances the nutritional quality and edible safety of camel milk by altering microbial diversity and gene functions. This study provides a foundation for exploring indigenous probiotic resources and promoting the industrial development of camel milk products.