Selenium (Se)-enriched plant polypeptide represents a premium selenium source possessing numerous physiological functions. Benzo(a)pyrene (BaP) is a carcinogenic food processing contaminant with hepatotoxic properties.The present study aimed to elucidate the mechanism underlying protective effects of selenium-enriched black soybean polypeptide (SeBSPP) against BaP-induced liver injury by integrating liver transcriptome, metabolomics, and gut microbiome. Our study revealed that SeBSPP effectively mitigated BaP-induced liver damage. SeBSPP suppressed the toxicity of BaP on the liver via inhibiting the formation of the carcinogen benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide-DNA (BPDE-DNA), reducing Aryl hydrocarbon receptor (AhR) enzyme activity and BaP related metabolic enzymes Cytochrome P450 Family (CYP450). Moreover, SeBSPP effectively inhibited liver lipid accumulation and reduced the risk of liver cancer by activating the major urinary proteins (Mups), regulating intestinal flora, and increasing the level of short chain fatty acids. Selenium-enriched yeast tablets also exerted a liver protection effect, albeit weaker compared to SeBSPP. This study provides a new direction for preventing hepatotoxicity of BaP and improves Se resource deficiency.