The interaction between calcium and magnesium as a risk modifier for cardiovascular disease (CVD) has been largely overlooked in previous studies, for the strict regulatory system in blood has been thought to keep such homeostatic interactions under tight control. This study aimed to investigate the association between calcium-magnesium ratio in hair and subclinical coronary artery calcification. Using multiple linear regression analysis, we examined the associations between calcium-magnesium ratio in hair and the coronary calcium score (CCS) in 216 Koreans aged 40 years and above (122 men and 94 women). We found that the calcium-to-magnesium ratio in hair was independently and positively associated with CCS after adjusting for age and sex (regression coefficient 6.051 ± 2.329, P = 0.010). When we assessed the association between the calcium-magnesium ratio and CCS after adjusting for potential cardiovascular risk factors and vascular function modifying drugs, we found that the strength of association with CCS was comparable to before (regression coefficient 5.434 ± 2.523, P = 0.032). Our findings suggest that among middle-aged and elderly Koreans without clinical CVD, the association between coronary artery calcification and hair calcium-magnesium ratio is stronger in those with a higher calcium-magnesium ratio in hair than in those with a lower ratio.