Objective To use liquid chromatography-mass spectrometry based plasma metabonomics to study the characteristics of human flora-associated (HFA) mice with coronary heart disease. Methods Twenty-eight female germ free C57BL/ 6J mice were divided into healthy control and coronary heart disease (CAD) groups. Each mouse was orally inoculated with a stool suspension from healthy people or patients with CAD to establish the HFA mouse models. At 6 and 10 weeks after inoculation, plasma metabolites were studied and PCA and PLS-DA statistical method were used to identify the characteristic metabolites. Results The PCA, PLS-DA and variable importance in projection analysis identified 30 characteristic metabolites present at 6 and 10 weeks after inoculation; structural identification found that L-carnitine, phenylpyruvic acid, and 1-naphthol, 2-naphthol were significantly higher in the CAD group compared with the control group. These potential biomarkers were related to the bile acid pathway and glycine, serine, threonine pathway. Conclusions The metabolism disorder in HFA mice appears similar to that of patients with CAD.