Miso is a traditional Japanese fermented food made by fermenting steamed soybean with koji (fermented cereals with Aspergillus oryzae). Many types of miso are produced in Japan, including miso with rice and/or barley depending on the region where it is produced. In this study, we used ¹H NMR metabolomic analysis to compare the characteristics of the components (metabolites) of miso with different ingredients. Three types of miso were compared: soybean miso, rice miso, and barley miso. After measuring the ¹H NMR of the aqueous solution of each miso, multivariate analysis of the spectral integration data was performed to compare the characteristic metabolites. Principal component analysis (PCA) showed a separation between soybean miso and rice, barley miso. Orthogonal Projection to Latent Structure Discriminant Analysis (OPLS-DA) extracted ethanol, saccharides such as glucose, and amino acids as metabolites contributing to the separation. Ethanol and glucose were higher in rice and barley miso, especially glucose in barley miso and ethanol in rice miso. Soybean miso was characterized by its high content of amino acids, including branched-chain amino acids. It was suggested that the characteristics of these ingredients were influenced not only by differences in ingredients, but also by the fermentation period and other factors. Although the number of metabolites that can be analyzed by ¹H NMR metabolomic analysis is smaller than that by GC/MS or LC/MS, it does not require any pretreatment and is easy to measure, so it can be applied to the comparison of food components and quality control, as in the analysis of miso components.