Artemisia species are widely used as food ingredients and raw material in traditional medicine. However, to date, the secondary metabolites of Artemisia gmelinii Weber ex Stechm. have not been sufficiently investigated. The secondary metabolites of A. gmelinii, which was collected from representative regions in Chungbuk, Gangwon, and Gyeongbuk, were analyzed using ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTof MS) combined with an unsupervised principal component analysis (PCA) multivariate analysis. In the loading scatter plot of PCA, significant changes in metabolites were observed between the regions, ten metabolites (3: 5-Ocaffeoylquinic acid, 4: 4-O-caffeoylquinic acid, 8: transmelilotoside, 12: quercetin 3-O-hexoside, 15: 3,4-O-dicaffeoylquinic acid, 17: 3,5-O-dicaffeoylquinic acid, 18: 4,5-O-dicaffeoylquinic acid, 19: syringaldehyde, 20: caffeoylquinic acid derivative, and 23: icariside II) were evaluated as key markers among twenty-five identified metabolites. Interestingly, the contents of the identified marker significantly differed between the three groups. This is the first study to report the presence of marker metabolites and their correlating geographical cultivation in A. gmelinii.