Former evidence regarding the associations of serum calcium (Ca) and magnesium (Mg) levels with apolipoproteins (Apos) in Chinese adults with coronary artery disease (CAD) were scarce. A total of 6781 patients with CAD were included in this cross-sectional study; mean age was 61.0 years. The associations of serum Ca, Mg, and Ca/Mg ratio with Apos (e.g., ApoA1, ApoB, and ApoB/A1 ratio) were determined using multivariate analysis of covariance. Serum Ca, Mg, and Ca/Mg ratio tended to have positive associations with ApoA1, while negative associations of serum Ca, Mg, and Ca/Mg ratio with ApoB and ApoB/A1 ratio were detected. In multivariate analysis, serum Ca, Mg, and Ca/Mg ratio were positively associated with ApoA1 levels (Q [quintile] 5 vs. Q1: 1.245 vs. 1.151 g/L for Ca, 1.207 vs. 1.188 g/L for Mg, 1.202 vs. 1.171 g/L for Ca/Mg ratio). In contrast, negative associations of serum Mg and Ca/Mg ratio with ApoB and ApoB/A1 ratio were shown. The corresponding ApoB and ApoB/A1 ratio values were 0.856 (vs. 0.887 g/L) and 0.728 (vs. 0.771) for Mg, and 0.814 (vs. 0.854 g/L) and 0.695 (vs. 0.751) for Ca/Mg ratio in Q5 compared with Q1. Serum Ca was inversely associated with ApoB and ApoB/A1 ratio (Q5 vs. Q4: 0.804 vs. 0.847 g/L for ApoB; Q5 vs. Q1: 0.662 vs. 0.732 for ApoB/A1 ratio). Path analysis showed that mediating effects of BMI on the "Ca or Mg-Apos" associations were not found. In summary, serum Ca and Mg tended to have positive associations with ApoA1 levels in patients with CAD, but had inverse associations with ApoB levels and ApoB/A1 ratio. Serum Ca/Mg ratio may be a more precise marker than serum Mg or serum Ca measures alone in assessing Apos measures of CAD risk.© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.