This article studied the effects of high L-carnitine consumption on intestinal microbiota, liver function, and metabolite distribution in mice. 16S rRNA results showed that high L-carnitine supplementation could induce the accumulation of Anaerobiospirillum, Coriobacteriaceae, Akkermansia_muciniphila, and Helicobacter. High intake of L-carnitine also induced liver injury, which was proved by the increases in the serum AST and ALT activities, production of inflammatory liver cytokines (IL-1, IL-6, TNF-α, and TNF-β), lipid metabolism (TC, TG, HDL, and LDL) disorder, and decline in antioxidant ability (SOD, GSH-Px, MDA, and RAHFR). The correlation analysis results showed that Anaerobiospirillum, Akkermansia_muciniphila, and Helicobacter were strongly positively correlated with AST, IL-1, TNF-α, TNF-β, and MDA levels (r > 0.5, p < 0.01 or p < 0.05). All in all, high Lcarnitine ingestion could induce a decline in the liver function by disorder in the gut bacteria composition, resulting in an increase in TMAO metabolism.