In this study, Lactobacillus plantarum (LP), alone or in combination with Streptococcus thermophilus, was used to ferment yam juice. Changes in the composition (phenols, organic acids, reducing sugars and volatile substances) and functional characteristics (antioxidative activity and ability to regulate the intestinal flora) of yam juice during fermentation were investigated. The results showed that the total phenolic (TP) content increased from 201.27 to 281.27 and 285.77 μg/mL for LP- and L. plantarum and S. thermophilus (LPST)-fermented yam juice, respectively. The antioxidative activity of yam juice improved significantly after fermentation, highly correlating with its TP content. In addition, LP- or LPST-fermented yam juice had positive effects on members of the human intestinal flora, improving the activity of Bifidobacterium and inhibiting the growth of Escherichia coli. Sensory analysis showed that LPST-fermented yam juice had a highest score. The results of this study showed that fermented yam juice can serve as a healthy beverage for consumers with low immunity or an imbalance of the intestinal flora.