It is thought that calcium and magnesium may be related to metabolic disorders such as obesity and metabolic syndrome; however, to date, there have been few studies investigating the association between serum calcium and magnesium levels and metabolic syndrome in middle-aged male adults. We aimed to investigate the association between serum calcium and magnesium levels and metabolic syndrome in Korean middle-aged male adults. Study subjects included 213 men aged 3060 years. MetS risk score is determined by adding the number of risk factors, waist circumference, triacylglyceride (TG), HDL cholesterol, glucose, and blood pressure (BP). The study population was divided into three groups according to the MetS risk score: group I (MetS risk score a parts per thousand currency sign1; n = 106), group II (MetS risk score = 2; n = 51), and group III (MetS risk score a parts per thousand yen3; n = 56). The serum Ca, according to increase of MetS risk score, was significantly higher (p < 0.001), and there was no significant difference in serum Mg concentration among the three groups. Subjects with high TG and high BP had higher serum calcium levels than those without such abnormalities. Subjects with higher glucose had lower serum magnesium levels than those without such abnormality. The correlation analysis indicated that the serum Ca had positive correlations with the MetS risk score (r = 0.1769, p < 0.01), serum TG (r = 0.2516, p < 0.001), and DBP (r = 0.2246, p < 0.01). The correlation analysis indicated that the serum Mg had an inverse relationship with serum glucose (r = -0.2404, p < 0.001). In conclusion, serum Ca had positive association with TG and BP, while serum Mg had negative association with serum glucose after adjusting age and BMI among the middle-aged Korean male adults.