Monascus rice (MR) and highland barley monascus (HBM), the monascus fermented products, are applied in food and medicine to reduce cholesterol and promote digestion. Due to the fermentation substrates, their compositions are different. However, the exact differences have not been reported to date. By UPLC-Q-Orbitrap HRMS analysis, multiple components of twenty batches of MR and HBM samples were identified. In total, 100 components were confirmed (e.g., monacolins, pigments, decalin derivatives, amino acids). Then, principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) were used to filter the components of MR and HBM. In the PCA model, 88.1% of the total variance was uncovered. The OPLS-DA model showed better discrimination between MR and HBM, and the values of R2X, R2Y, and Q2 were 0.837, 0.996, and 0.956, respectively. Based on the value of the variable importance in projection (VIP) and the result of the t-test, 424 components (VIP > 1, p < 0.05) were acquired. Finally, 11 differential components were selected as the characteristic compounds to discriminate between MR and HBM: the content of 9 monacolins (3-hydroxy-3,5-dihydrodehydromonacolin K, monacolin K, dehydromonacolin K, dehydromonacolin J hydroxy acid, monacophenyl, dihydromonacolin J hydroxy acid, monacolin L, dehydromonacolin J, and monacolin R) in HBM was higher than the content in MR, but the content of 2 pigments (ankaflavin and monascin) was lower in HBM and higher in MR. The findings revealed the similarities and differences in the chemical composition between MR and HBM, which is expected to provide a basis for quality control of HBM.