Black and red rice have many physiological effects, including antioxidant capacity and decreasing blood glucose, because they are flavonoid-rich. Here, our study found that Hongcaomi (a red rice variety) of five examined rice cultivars contained the highest total polyphenol content and total flavonoid content and the strongest antioxidant activity, with values of 5.83 mg GAE/g, 1.57 mg RE/g, and 72.63 μmol Trolox/g, respectively. The decreased blood glucose effect showed that the strongest effect was shown by the two red rice cultivars, followed by the black rice cultivar Ashamurasaki, the white rice cultivar Yixiang1B, and the black rice cultivar Chongxuehei which had no effect. The study further found that the strongest physiological effect in red rice was derived from catechin. In addition, our study reveals that pigmented rice could decrease blood glucose levels through many pathways, including repairing liver morphology, improving the expression level of genes involved in gluconeogenesis and glycogenesis pathways, and regulating the composition of the gut microbiota.