Liquid-liquid microextraction (LLME) combined with gas chromatography/mass spectrometry (GC-MS) was used to analyze the base distillates produced by five different layers of Jiupei in the same cellar of Gujinggongjiu ,and selected 25 kinds of reported biologically active compounds for quantification. The spiked recovery of the compounds were between 82.22% and 105.83%, and the order of total contents in the 5 base distillates was A> C> E> B> D. Principal component analysis was used to analyze the quantitative results of 25 kinds of biologically active compounds. The results showed that: A produced by the uppermost Jiupei differed greatly from the rest of the samples, and was distinguished on the second principal component; B, C, D, E had certain similarities on the second principal component and showed differences on the first principal component. This study was helpful for understanding the differences in bioactive substances among different base distillates.