In this study, the quality changes of fresh-cut yam slices treated with a mixture of ethanol (25%, w/w) and ascorbic acid (1%, w/w) treatments (EA) were assessed, and the bacterial community composition and their metabolic functions for these samples were investigated. Results showed that EA washing treatment notably reduced the respiratory intensity and microbial growth of fresh-cut yams in packaging during refrigeration, maintained the tuber firmness, and delayed discoloration. Proteobacteria was the main phyla significantly associated with off-flavor of yams, Bacteroidetes was the sensitive genera and was positively correlated to CO2 content of the packaging bag and sensory evaluation of yams. Interestingly EA could specifically remove the pathogenic bacteria of Pseudomonas (Proteobacteria), greatly destroy the stability of the bacterial community network on the fresh-cut yam slices’ surface, and achieve a better antibacterial effect. EA washing treatment reduced the metabolic capacity of bacterial community and was helpful to delay the aging and spoilage of fresh-cut yams, meanwhile, significantly inhibited transferase expression, and could help to maintain the quality of the fresh-cut yams. In conclusion, ethanol and ascorbic acid mixture washing agent altered the successional process of bacterial communities to reduce the pathogenic bacteria of fresh-cut yams during cold storage. •Ethanol-containing washing could destroy the stability of bacterial community network of yams.•Has correlation between quality and microbial composition of yams, especially Proteobacteria.•Ethanol-containing treatment inhibit the expression of transporter genes in microorganisms.