Low magnesium (Mg) and high calcium (Ca) levels are linked to increased cardiovascular disease (CVD) risk in the general population. This prospective study assessed whether there are any independent associations of serum Mg levels and Ca-Mg ratios with mortality in patients with coronary artery disease (CAD). This prospective cohort study included 3380 CAD patients. Cox regression models were used to estimate associations of serum Mg and Ca-Mg ratio with risk of mortality. A total of 562 deaths (331 due to CVD) were recorded during a 7.59-year (median) follow-up. Spline plots displayed U-shaped associations between serum Mg levels and Ca-Mg ratios and risk of mortality. When compared with a moderate group, adjusted hazard ratios (95% confidence intervals) for low Mg levels and high Ca-Mg ratios were 1.59 (1.30-1.95) and 1.31 (1.06-1.61) for all-cause mortality, and 1.71 (1.32-2.22) and 1.44 (1.09-1.89) for CVD mortality, respectively. There was also a tendency to increase risk of mortality in patients with high serum Mg levels and low Ca-Mg ratios. Associations of low serum Mg and high Ca-Mg ratio with risk of mortality did not change when stratified by gender, body mass index, CAD type, estimated glomerular filtration rate, use of diuretics, or history of diabetes or hypertension. This study demonstrated that a moderate Ca-Mg ratio (range: 3.91-4.70) had the lowest mortality risk, and that low serum Mg and high Ca-Mg ratio were independent risk factors of mortality in CAD patients. Nevertheless, the optimal dose-response of Mg and Ca for mitigating CAD risk still requires further investigation.