Barley (Hordeum vulgare) is a major cereal grain grown in temperate climates globally and provides various nutrients in a peeled form after milling. However, milling causes changes in nutritional composition, including metabolites. Thus, a metabolomics study was conducted to monitor the changes in nutritional composition before and after the milling of Hordeum vulgare seeds (Saechalssal, Hinchalssal, and Yeongbaekchal) focusing on the development and application of new analytical methods for organic acids (OA) and amino acids (AA). Profiling analyses of OAs and AAs were performed using GC-MS/MS. This analytical method showed good linearity (r ≥ 0.995) with limit of detection (0.1 ng, 21.2 ng) and limit of quantitation (0.3 ng, 63.6 ng), respectively. Repeatability varied from 0.1 to 12.4 (% RSD) and accuracy varied from –12.3 to 14.8 (% RE), respectively. Altered levels of 36 metabolites (16 OAs, 20 AAs) were monitored post-milling and compared with pre-milling in the three Hordeum vulgare cultivars. Radar plots of OAs and AAs to corresponding mean levels of each pre-milling group in the three Hordeum vulgare cultivars were easily distinguished from those in each post-milling group. The pre-and post-milling groups of the three Hordeum vulgare cultivars were completely separated by partial least square discriminant analysis, and the lysine, cysteine, glutamic acid, asparagine, 4-hydroxyphenylacetic acid, and citric acid were significantly different. Therefore, this study will be useful for monitoring altered metabolites following milling and discrimination of varieties.