The gut microbiota and it´s metabolism are vital targets of probiotics regulating high fat-diet (HFD) induced hyperlipidemia, which can relieve the pressure caused by the striking growth of sub-health people. Pediococcus pentosaceus PP04 (PP04) could colonize in intestine to regulate gut microbiota and it´s metabolites directly, the rebalanced intestinal flora mediated by PP04 could facilitate the secretion of short chain fatty acids to control body weight gain, PP04 intervention also changed bile acids (BAs) profiles and enhanced the ileal concentrations of antagonists including tauro-α/β-muricholic acid sodium salt and ursodeoxycholic acid to inhibit intestinal farnesoid X receptor/fibroblast growth factor 15 (FXR/FGF15) signaling coupled with the activation of hepatic FXR/small heterodimer partners signaling (SHP), which accelerated the hepatic BAs de novo synthesis and excretion with feces to eliminate HFD caused hyperlipemia effectively. This study provided important evidence regarding PP04 as dietary supplement to relieve hyperlipidemia by influencing BAs enterohepatic circulation.