Subclinical hypothyroidism has been associated with dyslipidemia, hypertension, and increased risk of coronary artery disease. However, limited is known for its effect on renal function. Here we aimed to investigate whether subclinical hypothyroidism is associated with reduced estimated glomerular filtration rate (eGFR) and proteinuria in the general population. A cross-sectional cohort of 74,356 adults aged ≥20 year participating in voluntary health examinations without previous thyroid diseases were recruited in Taiwan. The mean eGFR of persons with euthyroidism, subclinical, and overt hypothyroidism are 87.99, 83.46, and 72.22 mL/min/1.73 m2, respectively (P-for- trend < 0.001). The proportion of proteinuria in persons with euthyroidism, subclinical and overt hypothyroidism is 1.29%, 2.2%, and 2.97%, respectively (P-for-trend: 0.001). The odds ratio of CKD for subclinical, clinical, and all hypothyroidism is 2.04 (95% confidence interval (CI): 1.67-2.50) and 7.61 (95% CI: 4.92-11.77), and 2.41 (95% CI: 2.01–2.89), respectively as compared to euthyroidism. These odd ratios remained significant after further adjustments. The odds ratios for proteinuria is 2.04 (95% CI: 1.67–2.50), 7.61 (95% CI: 4.92–11.77), and 2.41 (95% CI: 2.01–2.89) for subclinical, clinical, and total hypothyroidism, respectively, although the odds ratios were attenuated after further adjustment. Our results suggest subclinical hypothyroidism is a novel risk factor of reduced renal function but not proteinuria.