Cyanidin‐3‐O‐glucoside (C3G), an abundant and widely utilized anthocyanin monomer, has been shown to significantly inhibit cholesterol absorption. Building on our previous research demonstrating the role of Lactobacillus as a specific intestinal microflora associated with C3G‐mediated cholesterol absorption inhibition, the present study aimed to evaluate the inhibitory effects of C3G on high‐fat diet–induced cholesterol absorption. Results indicate that C3G significantly reduced total cholesterol and triglyceride levels while suppressing red grease formation in Caco‐2 cells. In vivo, C3G ameliorated blood lipid levels and mitigated small intestinal damage, as evidenced by restored villus length and basal thickness. Additionally, C3G upregulated intestinal farnesoid X receptor (FXR) mRNA expression and inhibited the expression of key cholesterol absorption proteins, Niemann‐Pick C1‐Like 1 and acetyl‐CoA acetyltransferase 2. Furthermore, C3G increased short‐chain fatty acid content and activated ileal bile acid‐binding protein expression. C3G also inhibited intestinal bile acid (BA) reabsorption, promoted fecal BA excretion, and obstructed cholesterol emulsification. Moreover, C3G modulated gut microbiota abundance and diversity, increasing the abundance of Akkermansia, Bifidobacterium, Coprococcus, Ruminococcus, and Butyricicoccus. In conclusion, our findings suggest that C3G inhibits cholesterol absorption by reshaping intestinal flora composition and regulating the FXR‐BAs axis. This study provides a theoretical foundation for the use of C3G as a raw material for inhibiting cholesterol absorption.