Few studies have explored the association between mineral intake and chronic kidney disease (CKD). A cross-sectional analysis investigated the association between mineral intake (calcium, phosphorus, sodium, potassium, iron, and zinc) and CKD using the Health Examinee (HEXA) cohort of the Korean Genome and Epidemiologic Study (KoGES). For 159,711 participants, mineral intake was assessed by a food frequency questionnaire. CKD was defined as an estimated glomerular filtration rate (eGFR) of less than 60 mL/min/1.73 m2. Dietary intake of each mineral was divided into quartiles and the quartile including recommended dietary allowance (RDA) or adequate intake (AI) of each mineral was used as a reference. We assessed the association between the quartile of mineral intakes and CKD using polytomous logistic regression models. The lowest quartiles of phosphorus (≤663.68 mg/day, odds ratio [OR] = 1.64, 95% confidence interval [CI]: 1.25–2.15), potassium (≤1567.53 mg/day, OR = 1.87, 95% CI: 1.27–2.75), iron (≤6.93 mg/day, OR = 1.53, 95% CI: 1.17–2.01), and zinc (≤5.86 mg/day, OR = 1.52, 95% CI: 1.02–2.26) were associated with higher odds for advanced CKD compared with the references. The present study suggests that an inadequate intake of some minerals may be associated with CKD occurrence in the general population. Due to the reverse causation issue in this cross-sectional study design, further longitudinal prospective studies are needed in order to prove the results.