To investigate the biocontrol mechanism of Wickerhamomyces anomalus against postharvest diseases in peach fruits, this study investigated how W. anomalus influences the microbiome on the peach surface at a molecular level. Our results demonstrated that W. anomalus treatment significantly decreased the natural decay incidence of peach fruit by 38.88% during storage, while preserving fruit quality and nutritional stability. The treatment increased the diversity and richness of the bacterial community but decreased those of the fungal community, with more pronounced restructuring effects on the fungal community. W. anomalus reshaped the microbiome by establishing its dominance and suppressing key pathogenic fungi such as Alternaria, Cladosporium, and Fusarium. Furthermore, the treatment promoted the successional dynamics of beneficial bacterial genera, including Pseudomonas, Methylobacterium-Methylorubrum, Curtobacterium, and Hymenobacter, as well as beneficial fungal genera such as Golubevia and Acremonium. These findings indicate that W. anomalus achieves synergistic control of postharvest decay in peach fruits through direct suppression of pathogenic fungi and systematic modulation of the microbial community structure.