The ageing process has a significant impact on the aroma of Chinese Baijiu, which could strengthen the desirable flavor characteristics and reduce the undesirable ones. The aim of this study was to observe the initiation of meaningful changes in volatile fraction and locate the ageing markers during ageing storage of Chinese Highland Qingke Baijiu.

Samples of Chinese Qingke Baijiu were aged for 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, and 11 months before analysis. The samples were isolated by liquid–liquid extraction and then analyzed by comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry. The acquired data were processed by untargeted and targeted metabolomics approach to locate the ageing markers.

The untargeted metabolomics analysis (hierarchical clustering analysis, HCA) shows that the chemical composition of Qingke Baijiu presents a statistically significant deviation from the reference scenario after 5 months. Subsequently, supervised statistics analysis (orthogonal partial least squares discrimination analysis) was performed to locate the markers, which changed significantly during ageing. Fifteen markers were located, and seven of them were acetals. Notably, 1,1-diethoxy-propane, 1,1-diethoxy-butane, and 1,1-diethoxy-3-methyl-butane are important contributors to the flavor of Chinese Baijiu. The identified markers were applied for the untargeted metabolomics (HCA), and the results revealed that these markers could divide the Qingke Baijiu into two ageing stages, 0–5 months and 6–11 months.

The results suggest that it is a valuable tool for monitoring the changes of volatile compounds and locating the age markers in Chinese Baijiu.