The melanoidins were isolated from heat-moisture treated ginseng to explore its structural features and the preventive effect on red meat (RM) induced atherosclerosis (AS) in mice. Ginseng melanoidins isolates showed an average molecular weight (Mw) of 6.8 kDa and was mainly comprised of glycosylated proteins by Maillard reaction upon heat-moisture treatment, possessing CO, CN and NH groups. Afterwards, the inhibitory effect of melanoidins isolates supplementation on choline metabolism was further studied. Results demonstrated that melanoidins isolates diets could reduce levels of trimethylamine (TMA) and trimethylamine N-oxide (TMAO) by 21.24 % and 50.02 %, respectively. Diet supplementation of melanoidins isolates activated the intestinal epithelial adenosine monophosphate-activated protein kinase (AMPK) pathway with decreased energy intake, fecal pH, and levels of serum lipid and cholesterol. Melanoidins isolates feeding also increased the contents of short-chain fatty acids (SCFAs). The findings indicate melanoidins isolates may inhibit choline metabolism by co-regulating gut microbiota and the AMPK pathway.