Chinese yam (Dioscorea opposita Thunb.), as one of the medicinal and edible homologous plants, is rich in various nutrients and functional factors. In this study, Chinese yam fermented by Saccharomyces boulardii was performed to investigate its bioactive components and metabolic profile. And then, the main bioactive components and biological activities of fermented Chinese yam ethanol extract (FCYE) were evaluated. Results showed that there were 49 up-regulated metabolites and 52 down-regulated metabolites in fermented Chinese yam compared to unfermented Chinese yam. Besides, corresponding metabolic pathways analysis initially revealed that the distribution of bioactive substances was concentrated on alcohol-soluble small molecular substances. Ulteriorly, the total polyphenol content and the total flavonoid content in FCYE were significantly increased, and the corresponding antioxidant and immunomodulatory activities in vitro were also significantly enhanced. Our study provided a new reference for the comprehensive utilization of Chinese yam and laid a theoretical foundation for the development and application of natural probiotic-fermented products.