Huangshui (HS) is a key byproduct of Chinese strong-flavor Baijiu (a traditional distilled spirit) fermentation. This study investigated microbial succession and flavor formation across five key fermentation stages using high-throughput sequencing, physicochemical analysis, and untargeted GC-MS. The results show that Lactobacillus dominated the bacterial communities, while Thermoascus, Aspergillus, and Candida were core fungal genera. Redundancy analysis (RDA) identified acidity, available phosphorus, and ammonia nitrogen as the primary physicochemical drivers of microbial succession. Untargeted metabolomics detected 300 volatile compounds, with 29 discriminant volatile metabolites (VIP > 1.0 or p < 0.05), mainly enriched in carbohydrate and amino acid metabolism pathways associated with Lactobacillus, Thermomyces, Wickerhamomyces, and Kazachstania. These findings establish a link among physicochemical properties, microbiota assembly, and flavor metabolism, providing potential targets for optimizing Baijiu fermentation quality.