Lactic acid bacteria strain (LAB) NCU116 fermented Asparagus officinalis polysaccharides (FAOP) have been proven to cause substantial changes in physicochemical properties such as monosaccharide composition and molecular weight, accounting for their enhanced immune activity than unprocessed Asparagus officinalis polysaccharides (AOP). In the current study, the hepatoprotective effects of FAOP in mice with cyclophosphamide (CTX)-induced hepatotoxicity were investigated. FAOP were more effective than AOP in alleviating CTX-induced hepatic damage, including inhibition of hepatic biochemical markers (ALT, AST, AKP and LDH) and pro-inflammatory cytokines (TNF-α and IL-1β) as well as reinforcement of antioxidant systems (T-AOC, SOD, CAT, and MDA). In particular, compared with AOP, FAOP showed superior performance by promoting GSH biosynthesis, and normalizing the expression level of bile acid receptors (FXR and SHP) and key enzymes in bile acid synthesis (CYP7A1, CYP8B1 and CYP27A1). Modulation of disordered homeostasis of bile acids by FAOP can be attributed to the upregulation of hepatic short chain fatty acid (SCFA) receptors GPR41 and GPR109A as well as intestinal SCFA production. Furthermore, serum metabolomics study validated the hepatoprotective superiority of FAOP than AOP with evidence from variations in bile acid compositions and the construction of related metabolic pathways. Therefore, LAB NCU116 fermentation of Asparagus officinalis was practical and effective to obtain promising hepatoprotective polysaccharides, which might arise from enhanced SCFA production than unprocessed AOP.