Chronic kidney disease (CKD) and hypothyroidism are prevalent chronic conditions with a generally believed correlation between them. However, large-scale population studies and investigations into causation are lacking. This study analyzed CKD and thyroid function data from the National Health and Nutrition Examination Survey database spanning 2007 to 2012 using multiple regression analyses to examine the correlation between CKD and hypothyroidism. Bidirectional Mendelian randomization analysis was employed to investigate the causal association between the two conditions. As CKD stages deteriorated, there was a significant decrease in total triiodothyronine (TT3) and free triiodothyronine (P < .05). However, no significant decrease was observed in total thyroxine and free thyroxine. Notably, there was a significant increase in thyroid-stimulating hormone levels (P < .05). However, no significant changes were observed in thyroglobulin, thyroglobulin antibody, and thyroid peroxidase antibody levels. A causal relationship between CKD and reduced thyroid function was observed (odds ratio [OR] = 1.0041, 95% confidence interval [CI]: 1.0007–1.0075, P = .0186). Conversely, reverse causality was not statistically significant (OR = 2.540, 95%CI: 0.8680–4.8603, P = .1014). As CKD progressed, the risk of hypothyroidism increased. A causal correlation was observed between CKD and reduced thyroid function. Chronic kidney disease (CKD) and hypothyroidism are prevalent chronic conditions with a generally believed correlation between them. There is no large-scale population studies and the causation relationship between CKD and hypothyroidism are lacking. The finding of the causal relationship between CKD and hypothyroidism may be beneficial to the prevention of the disease and the prognosis of the patients.