The effects of different proportions of dietary sorghum rice and black rice on the expression of genes related to cholesterol metabolism in mice liver, intestine, and the characteristics of the small intestinal microbiota were investigated. Six types of diets were used to feed C57BL/6 mice: AIN-93M standard diet, high-cholesterol model diet, high-cholesterol and low-dose sorghum grain or black rice diet, and high-cholesterol and high-dose sorghum grain or black rice diet. The results showed that black rice or sorghum grain diets had no effect on the serum TC, LDL-C levels in the hypercholesterolemic mice, whereas these diets decreased serum TG level, and black rice diets increased serum HDL-C level. The diets containing black rice and sorghum grain had no effect on liver TC, TG, HDL-C levels. However, these diets decreased LDL-C levels significantly except high dose of black rice. The black rice or sorghum grain diets reduced the expression of the genes encoding liver 3-hydroxyl-3-methyl-glutarate monoacyl coenzyme A reductase (HMG-CoA-R) and increased the expression of SREBP-2, thereby partially inhibiting the synthesis of cholesterol in liver. The diets containing different proportions of black rice and a low proportion of sorghum grain reduced the expression level of Niemann-Pick type C 1 like 1 (NPC1L1) mRNA and increased the mRNA level of the ATP-binding cassette transporters, ABCG5/ABCG8, in the small intestine, thereby reducing cholesterol absorption. A diet containing a low proportion of black rice promoted the expression of ABCA1 mRNA and increased the expression of high-density lipoprotein (HDL) mRNA, thereby promoting reverse cholesterol transport. Black rice diets significantly increased the relative abundances of microbiota in the small intestine and maintained biodiversity, while sorghum grain had no positive effect on the abundance of microbiota.