L-Carnitine can be metabolized to trimethylamine (TMA) by gut microbiota and further converted into trimethylamine N-oxide (TMAO) in the liver, leading to liver damage. This study aimed to investigate the protective effect of quercetin against high L-carnitine-induced liver toxicity in mice. 3% L-carnitine drinking water was used to feed mice in this study. The formation of TMAO in the blood circulation of the tested mice was down-regulated following quercetin treatment. Administration of quercetin could also effectively antagonize the liver injury caused by high L-carnitine intake, which was proved by the decreased serum AST and ALT activities and the reduced levels of inflammatory liver cytokines (IL-1, IL-6, TNF-α, and TNF-β). Moreover, quercetin exhibited a rebalancing effect on dyslipidemia (TC, TG, HDL, and LDL) and antioxidant abilities (SOD, GSH-Px, MDA, and RAHFR) in L-carnitine-treated mice. The results of hepatic H&E and Oil Red O staining further verified the liver injury of high L-carnitine-treated mice and the protective effects of quercetin. These findings suggested that quercetin could attenuate the hepatotoxic effects of the mice fed with a high L-carnitine diet via inhibiting the circulating TMAO formation.