As the main by-product of Chinese strong-flavor liquor, yellow water plays an important role in the formation of flavor components. Yellow water from different fermentation periods (30th day, 45th day, 60th day) was selected to analyze the aroma components by Headspace solid phase micro-extraction Gas Chromatography–Mass Spectrometry, and the microorganism community was evaluated by high-throughput sequencing technology and bioinformatics analysis of DNA. As the fermentation time was prolonged, the main flavor components significantly increased, and the amount of the common microbial population between yellow water and pit mud increased gradually. Among the common microorganisms, Lactobacillus accounted for the largest proportion, at about 56.96%. The microbes in the yellow water mainly belonged to Firmicutes. The abundance of Bacilli (the main bacteria) gradually decreased with time, at 87.60% at the 30th day down to 68.87% at the 60th day, but Clostridia gradually increased from 10.29% to 27.48%. At the genus level, some microbes increased significantly from the 30th day to 60th day, such as Caproiciproducens, which increased from 2.65% to 6.30%, and Sedimentibacter, increasing from 0.47% to 2.49%. RDA analysis indicated that the main aroma components were positively correlated with Clostridia and negatively correlated with Bacilli.