Abstract: The antibacterial mechanisms of yellow water from liquor fermentation were studied with Bacillus subtilis used as the experimental strain.Growth curve of Bacillus subtilis, the surface of the bacteria by means of the scanning electron microscope, the test of the conductivity of Bacillus subtilis, bacterial protein synthesis by SDS-PAGE, fluorescence microscopy and fluorescence spectrophotometer were used to investigate the antibacterial mechanism of yellow water.The resulted indicated that the yellow water could inhibit the logarithmic growth of Bacillus subtilis.The surface of the bacteria treated with yellow water was rough by means of the scanning electron microscope, while the surface of the bacteria in control group was smooth.Yellow water could not change the bacterial membrane permeability by the test of the conductivity of Bacillus subtilis. Yellow water could inhibit bacterial protein synthesis by SDS-PAGE and the band of Bacillus subtilis with yellow water turned lighter.Fluorescence microscopy and fluorescence spectrophotometer results showed that DAPI integrated with Bacillus subtilis and the quantity of DNA after treated with yellow water for 9 h and RNA after treated with yellow water for 3 h were reduced by 30.39% and39.64% respectively. The results showed that yellow water from liquor fermentation could inhibit the growth of bacteria significantly, the mechanisms of the inhibition activity may include inhibiting synthesis of nucleic acid and protein.