Aim The aim of the study was to investigate the relationship between the ApoC3 rs5128 polymorphism and plasma lipid levels and the severity of coronary stenosis in the coronary heart disease (CHD) patients with different body mass index (BMI) in Chinese Han population. Methods Three hundred and twelve CHD patients were divided into healthy weight group(205 patients) and overweight/obese group(107 patients). Physiological, biochemical and coronary angiographical data were collected for all patients. The severity of coronary stenosis was assessed by the Gensini scoring system. Genome DNA was extracted from peripheral blood leucocytes and the genotypes of the ApoC3 rs5128 polymorphism were determined by polymerase chain reaction-restriction fragment length polymorphism method. Results The overweight/obese patients had higher weight, BMI, prevalence of hypertension, triglyceride (TG), lipoprotein (a), TG/high-density lipoprotein cholesterol (HDLC), total cholesterol (TC)/HDLC, low-density lipoprotein cholesterol (LDLC)/HDLC and apolipoprotein B100 (ApoB100)/apolipoprotein AI (ApoAⅠ), and lower HDLC and ApoAⅠ than the patients with healthy weight (P<0.05). In healthy weight group, the G carriers had higher prevalence of hypertension than the patients with the CC genotype (P<0.05). In overweight/obese group, the G carriers had higher levels of TG and TG/HDLC than the patients with the CC genotype (P<0.05). In healthy weight group and overweight/obese group, there were no significant differences in the distributions of the genotypes or alleles of the rs5128 polymorphism among the tertiles of the Gensini scores. Conclusion The ApoC3 rs5128 polymorphism is significantly associated with plasma TG and TG/HDLC levels, but not with the severity of CHD.