The role of magnesium in anemia remains unclear. We aimed to investigate the prevalence of anemia and its association with serum magnesium in a nationally representative sample. A total of 8,511 participants aged 18 years and over were recruited in this cross-sectional survey in 2009. Anemia was defined as hemoglobin concentration less than 130 g/l for men and less than 120 g/l for women. Multiple logistic regression models were applied to explore the association of magnesium and anemia. The prevalence of anemia in total was 14.0% with 8.8% for men and 18.5% for women (P<0.0001), respectively. The interaction terms between magnesium and gender and ferritin were significant (P<0.001). In men with serum ferritin≥15 ng/ml, compared with the first quartile of magnesium, the odds ratios (ORs) and 95% confidence intervals (CIs) for those in the second, third, and fourth quartile of magnesium were 0.65 (0.46, 0.91), 0.77 (0.55, 1.09), and 0.63 (0.45, 0.89), respectively, after adjusting multiple confounders. Likewise, in women with serum ferritin≥15 ng/ml, the corresponding ORs (95% CIs) were 0.71 (0.56, 0.91), 0.64 (0.49, 0.84), and 0.53 (0.40, 0.71). The associations between magnesium and anemia were not significant in neither men nor women with serum ferritin<15 ng/ml. Serum magnesium was inversely associated with anemia in both men and women, in particular among adults with high serum ferritin levels.