Differences between the old and young pit mud in a pit cellar enlarged differences in Zaopei (ZP) fermentation to varying degrees, ultimately affecting the aromatic quality of the Baijiu that is produced. The whole fermentation process could be divided into two phases, namely phase I (0_15 days) and phase II (25_40 days) based on the dynamics of the diversity of microbial communities. Starch and reducing sugar in phase I were used more rapidly by microflora, leading to a higher ethanol production in ZP within an old pit mud (OZP) and a higher acidity in ZP within a new pit mud (NZP), and resulting in different microbial succession patterns therein. Lactobacillus became the dominant bacteria more rapidly in OZP but maintained its abundance in NZP. Monascus and Trichosporon were the unique dominant functional fungi observed in the phase II of OZP. Two bacterial and six fungal genera were identified as core functional microorganisms linked to the variations in volatile metabolites during the fermentation process, ultimately resulting in a higher ester content in OZP and improved liquor quality. This study demonstrated the effect of new and old pit muds on ZP fermentation, and its findings can guide the future artificial regulation of NZP.