Objective To assess the relationships between iodine biological exposure and subclinical thyroid dysfunctions. Methods The cross-sectional survey was performed to obtain the epidemiologic data of population in three communities with different iodine biological exposure: mild iodine deficiency [median urinary iodine concentration (MUI) of 50 99g/L], more than adequate iodine intake (MUI of 200-299 μg/L), and excessive iodine intake (MUI over 300 μg/L). Univariate and multivariate analysis (logistic regression analysis) were used to analyze the risk factors of subclinical hypothyroidism and subclinical hyperthyroidism. Results Logistic regression analysis with sex and age controlled suggested that more than adequate iodine intake (OR = 3.172, P = 0.0004) and excessive iodine intake (OR = 6.391, P = 0.0001) increased the risk of subclinical hypothyroidism, while excessive iodine intake decreased the risk of subclinical hyperthyroidism (OR = 0.218, P= 0.0001). Logistic regression analysis including interaction of iodine intake and antibodies [tryroid peroxidase antibody (TPOAb) and thyroglobulin antibody (TgAb)] suggested that excessive iodine intake was an independent risk factor of subclinical hypothyroidism (OR = 6.360, P = 0.0001), but independent protect factor of subclinical hyperthyroidism (OR = 0.193, P = 0.0001). More than adequate iodine intake and its interaction with TgAb increased the risk of subclinical hypothyroidism independently, in addition, it decreased the risk of subclinical hyperthyroidism at the present of TPOAb. Conclusion Both excessive iodine intake and more than adequate iodine intake could increase risk of subclinical hypo thyroidism, supplement of iodine should be controlled to ensure MUI within the safe range.