Aim To investigate the association between apolipoprotein (ApoM) gene and coronary heart disease (CHD) by detecting the polymorphism of ApoM rs707921 site. Methods The polymorphism of ApoM rs707921 site was detected by single fluorescent labeling probe technique in 111 cases of CHD patients and 248 cases of control group. The distribution of genotype and allele frequency was analyzed. Results The frequencies of ApoM rs707921 genotype (AA, AC and CC) were 1.8%, 13.5% and 84.7% in CHD group, 2.0%, 25.4% and 72.6% in control group, respectively, there was significant difference between the two groups (P＝0.039). The frequencies of A and C allele in ApoM rs707921 site were 8.6% and 91.4% in CHD group, 14.7% and 85.3% in control group, respectively, the difference between the two groups was statistically significant (P＝0.023). Triglyceride level of AC＋AA genotype was significantly lower than that of CC genotype in CHD group (P＝0.043). There was no significant difference in the severity of coronary artery lesion between different genotypes of rs707921 polymorphism in CHD group (P＞0.05). Conclusion A allele of ApoM gene rs707921 site may reduce the risk of CHD, but has nothing to do with the severity of coronary heart disease.