Baijiu is a unique and traditional distilled liquor in China. Flavor plays a crucial rule in baijiu. Up to now, the research on the flavor of baijiu has progressed from the identification of volatile compounds to the research on key aroma compounds, but the release mechanism of these characteristic compounds is still unclear. Meanwhile, volatile compounds account for only a tiny fraction, whereas ethanol and water account for more than 98% of the content in baijiu. By summarizing the ethanol–water hydrogen bond structure in different alcoholic beverages, it was found that flavor compounds can affect the association strength of the ethanol–water hydrogen bond, and ethanol–water can also affect the interface distribution of flavor compounds. Therefore, the research on ethanol–water microstructure in baijiu is helpful to realize the simple visualization of adulteration detection, aging determination and flavor release mechanism analysis of baijiu, and further uncover the mystery of baijiu.