The research on the influence of phase temperature storage technology on the microbial population structure on the surface of daylily provides a reference for the preservation of daylily. The daylily collected from Qingyang， Gansu was packaged in groups and stored in the refrigerator (4 ℃±1 ℃)， cold storage (0 ℃±0.5 ℃) and phase temperature environment (-0.5 ℃±0.1 ℃). The browning was measured at 7 days， and extracting surface microbial samples， using specific primers to perform PCR amplification on the V3-V4 region of the bacterial metagenomic 16S rRNA and the fungal metagenomic ITS1-1F region， analyzing the microbial relative abundance and diversity of daylily based on Illumina high-throughput sequencing technology. At the genus level， Dothideomycetes， Microbotryomycetes， Tremellomycetes， Eurotiomycetes， and Sordariomycetes are the dominant flora of daylily fungal communities， and Cyanobacteriia， Gammaproteobacteria， Alphaproteobacteria， Bacilli and Clostridia are the dominant flora of the daylily bacterial community. From the perspective of the number of OTUs in the dilution curve， the diversity of fungi and bacteria on the surface of daylily stored at phase temperature is the lowest， which proves that storage at phase temperature can effectively inhibit the diverse growth of surface microorganisms.