Our research group had shown that lotus seed resistant starch (LRS) had hypolipidemic effect, but its mechanism is still being studied. Bile acids are important metabolic pathway of cholesterol, accelerating the conversion of cholesterol into bile acids and excreting them in the fecal may be one of the effective ways to reduce cholesterol levels in the body. This study aimed to reveal the lipid-lowering effect of LRS from the perspectives of fecal microbiota and bile acids. Herein, a rat model of hyperlipidemia was established and intervened with LRS. Fecal samples from different periods were collected to study the changes in microbiota and bile acids, and the correlation network diagram was established to reveal the lipid-lowering mechanism of LRS. The results showed that LRS inhibited the growth of Prevotella and Allobaculum in hyperlipidemic rats. Meanwhile LRS promoted the excretion of cholic acid (CA), chenodeoxycholic acid (CDCA), alpha-muricholic acid (α-MCA), ursodeoxycholic acid (UDCA), ursocholic acid (UCA), 7-ketodeoxycholic acid (7-keto-DCA) in hyperlipidemic rats. Furthermore, total cholesterol (TCHO), low-density lipoprotein cholesterol (LDL-C) were negatively correlated with CA, CDCA, UDCA and UCA, and TCHO was positively correlated with Prevotella. Triglycerides (TG) was negatively correlated with CA, CDCA, 7-keto-DCA and UCA, while high-density lipoprotein cholesterol (HDL-C) was positively correlated with α-MCA. Regulating the gut microbiota such as Prevotella and accelerating the transformation of liver cholesterol into primary bile acids (CA, CDCA) for excretion from the body was one of the effective means for LRS to ameliorate blood lipid levels in hyperlipidemic rats.