As one of low-digestible proteins, tartary buckwheat protein (BWP) revealed a cholesterol-lowering activity. The relationship between the prevention of BWP on dyslipidemia and changes in the numbers of gut microbiota was investigated. The male C57BL/6 mice were separately fed on normal diet, high-fat diet (HFD) with casein, and HFD with BWP extract for 6 weeks. Quantitative PCR assay was applied to quantify the microbiota composition in feces. The levels of plasma total cholesterol (TC) and triglyceride (TG) in the mice fed on HFD with BWP were significantly lower than those on HFD with casein. BWP promoted the growth of Lactobacillus, Bifidobacterium and Enterococcus and inhibited the growth of Escherichia coli in HFD-fed mice. Moreover, Bifidobacterium population was closely related to contents of plasma lipids. Further, BWP significantly decreased the levels of plasma inflammation factors as induced by HFD, including lipopolysaccharide, tumor necrosis factor α and interleukin 6. BWP significantly increased the excretion of total bile acids and short-chain fatty acids in feces. In conlusion, BWP benefited cholesterol metabolism, which could be attributed to regulating composition of gut microbiota.