Poaceae practically dominate staple crops for humans. In addition to the issue of sustenance, there is a growing interest in the secondary metabolites of these staple crops and their functions on health. In this study, metabolomic variations were investigated among six important species of Poaceae with a total of 17 cultivars, including wheat, maize, rice, sorghum, foxtail millet, and broomcorn millet. A total of 201 flavonoid metabolites and 29 carotenoid metabolites were identified based on the UPLC-ESI-MS/MS system. Among them, 114, 128, 101, 179, 113, and 92 flavonoids and 12, 22, 17, 15, 21, and 18 carotenoids were found in wheat, maize, rice, sorghum, foxtail millet, and broomcorn millet, respectively. Only 46 flavonoids and 8 carotenoids were shared by the six crops. Crop-specific flavonoids and carotenoids were identified. Flavone, anthocyanins, flavanone and polyphenol were the major metabolite differences, which showed species specificity. The flavonoid content of the grains from 17J1344 (sorghum), QZH and NMB (foxtail millet) and carotenoids from Mo17 (maize) were higher than the other samples. This study provides a better knowledge of the differences in flavonoid and carotenoid metabolites among Poaceae crops, as well as provides a theoretical basis for the identification of functional metabolites in these grains.