Using functional microorganisms to control contamination is an effective way to control the biogenic amine content in Huangjiu production. Pontibacter beigongshangensis was a new microbial species isolated from Huangjiu koji, which could induce the production of bacteriocin by Pediococcus pentosaceus. Bacteriocins had inhibitory effects on Staphylococcus saprophyticus, Cronobacter sakazakii, Brevibacterium casei, Bacillus, and Enterobacter cloacae, which produce biogenic amines in Huangjiu. Meanwhile, Pontibacter beigongshangensis and Pediococcus pentosaceus do not produce biogenic amines. During Huangjiu fermentation, the natural enhanced Qu created by adding Pontibacter beigongshangensis and Pediococcus pentosaceus, could reduce the biogenic amines content by 29.8% in Huangjiu, but had little effect on the flavor quality of Huangjiu. Therefore, Pontibacter beigongshangensis and Pediococcus pentosaceus can be used as functional species for reducing biogenic amines in Huangjiu brewing.