Highland barley (HB, Hordeum vulgare L. var. nudum Hook. f.), also known as naked or hulless barley, is a kind of cereal crop growing at high altitudes (4200–4500 m) around the world. In this study, HB vinegar (HBV) was prepared, using Tibetan HB as the main raw material, according to the process of Shanxi aged vinegar (SAV), a famous vinegar in China, in which sorghum is usually used as the main raw material. The related main compounds, such as alcohol and acetic acid, in the alcohol and acetic acid fermentation processes were monitored and analyzed, respectively. The flavor components in the aged vinegars were analyzed by headspace solid-phase microextraction, combined with gas chromatography-mass spectrometry, and compared with sorghum vinegar (SV), which was made, using sorghum as the raw material, based on the SAV process. The results revealed that at the alcohol fermentation stage, the alcohol content of HB mash was higher than that of the sorghum mash (p < 0.05), and at the acetic acid fermentation stages of HBV and SV, the total acid contents were 6.23 and 5.81 (g·100 mL−1 and p < 0.05), respectively. After aging one and a half years, the contents of non-volatile acid, volatile acid, and ester compounds in HBV were higher than those in SV. Therefore, HB can replace sorghum as the raw material for making SAV. Based on a literature search, the comparison and analysis of the main components and volatile flavor compounds of HBV and SV were not studied before.