OBJECTIVE：To explore the genome-wide methylation differences between coronary heart disease（CHD）patients and healthy volunteers，and to investigate the relationsip of DNA methylation with CHD from epigenetics. METHODS：In case-control study，subjects were divided into CHD group（50 cases）and health control group（50 cases）. DNA of 2 groups were sequenced with methylated DNA immunoprecipitation sequencing technology. The genome-wide methylation differences were analyzed and compared between 2 groups. RESULTS：The number of methylation peak in CHD group was higher than health group，with statistical signficance（ P＜0.05）. The methylation peak mainly distributed in 5’UTR，Intron functional elements. The number of reads in AQP1，SHB and other gene promoters in CHD group were lower than health group，and its methylation level decreased. The number of reads in GRK5 and serveal gene promoters on chrX in CHD group were higher than helath group，and its methylation level increased，with statistical significance（P＜0.01）. CONCLUSIONS：The genome-wide methylation level of CHD patients are higher than those of healthy volunteers. The occurence of CHD is possibly associated with the change of methylation level of related gene promoters.