Background: Thyroid hormones (THs) are critical for brain development. Whether low-moderate fluoride exposure affects thyroid function and what the impact is on children's intelligence remain elusive. Objectives: We conducted a cross-sectional study to examine the associations between low-moderate fluoride exposure and thyroid function in relation to children's intelligence. Methods: We recruited 571 resident children, aged 7-13 years, randomly from endemic and non-endemic fluorosis areas in Tianjin, China. We measured fluoride concentrations in drinking water and urine using the national standardized ion selective electrode method. Thyroid function was evaluated through the measurements of basal THs [(total triiodothyronine (TT3), total thyronine (TT4), free triiodothyronine (FT3), free thyronine (FT4)] and thyroid-stimulating hormone (TSH) levels in serum. Multivariable linear and logistical regression models were used to assess associations among fluoride exposure, thyroid function and IQ scores. Results: In adjusted models, every 1 mg/L increment of water fluoride was associated with 0.13 uIU/mL increase in TSH. Every 1 mg/L increment of urinary fluoride was associated with 0.09 ug/dL decrease in TT4, 0.009 ng/dL decrease in FT4 and 0.11 uIU/mL increase in TSH. Fluoride exposure was inversely related to IQ scores (B = -1.587; 95% CI: -2.607, -0.568 for water fluoride and B = -1.214; 95% CI: -1.987, -0.442 for urinary fluoride). Higher TT3, FT3 were related to the increased odds of children having high normal intelligence (OR = 3.407, 95% CI: 1.044, 11.120 for TT3; OR = 3.277, 95% CI: 1.621, 6.623 for FT3). We detected a significant modification effect by TSH on the association between urinary fluoride and IQ scores, without mediation by THs. Conclusions: Our study suggests low-moderate fluoride exposure is associated with alterations in childhood thyroid function that may modify the association between fluoride and intelligence.