Taking the nine common microbial strains in liquor-making process as test objects, this paper studied the characteristics of phospholipid fatty acid (PLFA), a characteristic component of the strains cell membrane, and the relationships between the detected amount of PLFA and the biomass of the strains. There existed significant differences in the PLFA fingerprints between test bacteria, actinomycetes, molds, and yeasts, and the PLFA fingerprint of each strain could be used as the basis to distinguish species and genus. Within a certain range of the strains biomass, the detected amount of total PLFA or 16:0 was linearly correlated with the biomass. After adding different biomass Gram positive (G+) bacteria, Gram negative (G-) bacteria, and fungi in fermented grains, a significant difference was observed in the relative amount of PLFA between experimental and control samples. It was suggested that the fingerprint of PLFA could quantitatively or semi-quantitatively characterize the microbial community structure and its dynamic variation in fermented grains. By detecting the PLFA profiles of fermented grains in various liquor industries and by analyzing the microbial community structure in the fermented grains, it was substantiated that PLFA fingerprinting was of general applicability.