Among 12 aroma types of Baijiu, the strong aroma type of Baijiu (Nongxiangxing Baijiu) is well received by customers for its rich and full aroma profile. According to the aroma characteristics of different geographical locations, Nongxiangxing Baijiu can be divided into Jianghuai, Sichuan and North categories. However, the reasons for the differences in Nongxiangxing Baijiu flavor in different regions are still unclear. Hence, representative brands (i.e., Gujinggong, Luzhou Laojiao and Banchengshaoguo) of Nongxiangxing Baijiu from three representative regions were chosen to explore their differences in profile aroma compounds. In this study, a total of 50, 41, 35 potential aroma compounds in Banchengshaoguo, Gujinggong, and Luzhou Laojiao samples were respectively identified by direct injection combined with gas chromatography-olfactometry/mass spectrometry (GC-O/MS). Among them, 18 aroma compounds were further recognized as important aroma compounds owing to their high flavor dilution (FD) value, Osme value, and odor activity value (OAV) ≥ 1. Moreover, the relationship between the above potential aroma compounds and the aroma profile of the three representative samples was analyzed by molecular matrix analysis. The results showed that various aroma compounds contributed differently to the flavor characteristics of Nongxiangxing Baijiu. In particular, 13 aroma compounds were tentatively defined as crucial profile aroma compounds due to their high aroma expression intensity and remarkable contribution to the flavor characteristics of Nongxiangxing Baijiu in different regions, and these crucial profile aroma compounds may be the reason for the difference in aroma profile of Nongxiangxing Baijiu from distinct regions.