In this study, the microbial diversity of flowering cabbage incisions during cold storage, with special reference to the dynamic changes in the relative abundance of microflora, was analyzed by high-throughput sequencing. Flowering cabbage samples stored for 0, 7 and 14 days were collected, and the composition and abundance of microflora in the three samples were investigated and compared by analyzing the sequences of bacterial 16S rRNA and fungal internal transcribed spacer (ITS). The dominant fungal phyla were Basidiomycota, Ascomycota and unclassified Fungi during the whole storage time. The dominant bacterial phyla were Firmicutes and Proteobacteria during the early storage period, while Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes became dominant during the middle and late storage periods. Microbial diversity data showed that the diversity of fungi was higher than that of bacteria. The results of this study can provide theoretical support for future development of antibacterial agents and preservation technologies for flowering cabbage.