Rifampicin (RFP) is a well-known first-line antitubercular drug recommended by the World Health Organization. However, RFP-induced hepatotoxicity makes it impractical for use in long-term antitubercular therapy, and its mechanism is still incompletely understood. This study decrypts the mechanism of aberrant cholesterol metabolism in RFP-mediated liver injury and explores the protective effects of genistein (GEN), an isoflavone isolated from the dyer's broom plant (Genista tinctoria), when used in conjunction with RFP. RFP significantly promoted the formation of lipid droplets, increasing cholesterol deposition in liver by reducing cholesterol 25-hydroxylase (CH25H) and its downstream effector LXRα-ABCA to decrease cholesterol efflux. GEN upregulated CH25H and ultimately relieved RFP-induced liver injury; furthermore, replacing endogenous 25-hydroxycholesterol (25HC) both in vivo and in vitro accordingly rescued the hepatotoxicity induced by RFP. Finally, molecular docking and cellular thermal shift assay (CETSA) showed that RFP could bind to CH25H and impair its stability, an interaction that could be reversed by GEN. Thus, RFP restrains cholesterol efflux by reducing the CH25H-LXRα-ABCA axis to trigger steatosis, while GEN restores this pathway by upregulating CH25H, facilitating cholesterol efflux and mitigating RFP-induced liver injury.