Population-based studies on the association between cadmium (Cd) exposure and thyroid function are limited and have shown conflicting results. Two independent cross-sectional studies using different Cd biomarkers were carried out in six rural areas with different soil Cd levels in China. Thyroid dysfunction was defined based on levels of thyroid stimulating hormone (TSH) and free thyroxine (FT4). Both multivariable linear regression, multiple logistic regression and restrictive cubic splines models were used to estimate the association between Cd and thyroid dysfunction. For both of the two independent studies, higher Cd levels were observed to be associated with lower TSH levels and higher risk of thyroid dysfunction. The negative relationship between urinary Cd and TSH was found in both total participants (β = -0.072, p = 0.008) and males (β = -0.119, p = 0.020) but not in females, however, the negative relationship between blood Cd and TSH was only found in females (β = -0.104, p = 0.024). Higher urinary Cd (> 2.52 µg/g creatinine) was associated with higher risk of thyroid dysfunction, while higher blood Cd was associated with higher risk of hyperthyroidism status. The adjusted Odds Ratio (OR) for the risk of hyperthyroidism status was 3.48 (95%CI:1.36–8.92) and 6.94 (95%CI:1.23–39.31) times higher with every natural log unit higher in blood Cd in total participants and males, respectively. Results from the two independent cross-sectional studies consistently suggested that higher Cd levels were associated with sex-specific thyroid dysfunction.