This study aimed to observe the relationship between iodine nutrition status (dietary iodine intake and estimated iodine intake based on urinary iodine concentration (UIC)) and thyroid disease-related hormones. This study involved 6090 subjects >19 years old with valid UIC, assessed between 2013 and 2015 by the Korean National Health and Nutrition Examination Survey, using a stratified, multistage, clustered probability-sampling design. The estimated iodine intake in participants was measured using UIC and urine creatinine. To examine the effect of iodine intake on thyroid disease, the iodine intake was divided into Korean Dietary Reference Intakes groups, and logistic regression analysis was performed via the surveylogistic procedure to obtain odds ratios (ORs) and 95% confidence intervals (CIs). The estimated iodine intake showed a significant positive correlation with dietary iodine intake (r = 0.021, p < 0.001), UIC (r = 0.918, p < 0.001), and thyroid-stimulating hormone (TSH) (r = 0.043, p < 0.001), but a significant negative correlation with free thyroxine (FT4) (r = −0.037, p < 0.001). Additionally, as the estimated iodine intake increased, age, TSH, and UIC increased, but FT4 decreased (p for trend < 0.0001). The risk of thyroid disease was higher in the “≥tolerable upper intake level (UL ≥ 2400 µg/day)” group than in the “<estimated average requirement (EAR < 150 µg/day)” group in females (OR: 2.418; 95% CI: 1.010–5.787). Also, as iodine intake increased, the risk of thyroid disease increased (p for trend < 0.038).