Fermented grain (Zaopei) is the main microbial habitat and biochemical reaction system of health factors for Wuliangye-flavour liquor fermentation. In the present work, the bacterial communities in four depths of Zaopei, from the same fermentation pit, aged over 60 years, and amino acids as major health factors in four liquors from directly corresponding Zaopei were investigated by Illumina MiSeq sequencing and liquid chromatography mass spectrometry (LC-MS), respectively. Results showed that a total of 18 amino acids were detected in the four liquors, and eight dominant bacterial genera were observed in four Zaopei corresponding to the four liquors. Meanwhile, total amino acids, 12 amino acids (Glu, Asp, Val, Ile, Cys, Met, Lys, Arg, Gly, Ala, Tyr, and Thr), bacterial richness, and the percentages of Lactobacillus and Pseudomonas increased with the increase in Zaopei’s depth; five amino acids (Cit, Phe, Leu, Pro, and Ser), and the percentages of Pediococcus and Bacteroides, first increased and then decreased, with the increase in Zaopei’s depth. Moreover, the 12 amino acids were significantly (p < 0.01) and strongly (|ρ| > 0.8) positively correlated with Lactobacillus and Pseudomonas. Therefore, these results can provide relevant data support for increasing amino acid content in Wuliangye-flavour liquor.