An increasing number of studies have revealed that phthalate exposure alters thyroid hormone homeostasis in the general population, but there is insufficient evidence of the effect of longitudinal maternal phthalate exposure on maternal and fetal thyroid hormones during pregnancy. We longitudinally assessed the effect of prenatal phthalate exposure in pregnant women on umbilical cord and maternal thyroid hormones at three trimesters during pregnancy. We recruited 98 pregnant women and collected urine and blood samples at three trimesters in an obstetrics clinic in Southern Taiwan from 2013 to 2014. We analyzed the concentrations of 11 urinary phthalate metabolites, including monoethylhexyl phthalate, mono-(2-ethyl-5-oxo-hexyl) phthalate (MEOHP), mono-(2-ethyl-5-hydroxyhexyl) phthalate, mono-(2-ethyl-5-carboxypentyl) phthalate (MECPP), mono-n-butyl phthalate, monoisobutyl phthalate (MiBP), monoethyl phthalate (MEP), using online liquid chromatography-tandem mass spectrometry. The cord and maternal serum levels of thyroxine (T), free T, triiodothyronine (T), thyroid-stimulating hormone (TSH), and thyroxine-binding globulin were measured using an electrochemiluminescence immunoassay. A mixed-model analysis was utilized to assess the effect of longitudinal phthalate exposure on thyroid hormones and adjusted for significant covariates. We found that urinary MiBP (β=-0.065, 95% confidence interval (CI): -0.124, -0.005), and MEOHP (β=-0.083, 95% CI: -0.157, -0.009) were significantly negatively associated with serum TSH. Urinary MECPP was inversely related to serum T (β=-0.027, 95% CI: -0.047, -0.006). Urinary MEP (β=0.014, 95% CI: -0.001, 0.028) and MiBP (β=0.033, 95% CI: 0.018, 0.049) were positively related to free T. We found that cord serum T (β=0.067, 95% CI: 0.003, 0.131) and free T (β=0.031, 95% CI: 0.001, 0.062) levels had significant positive associations with maternal ΣDBPm levels at the second trimester. We concluded that different phthalates exposure windows during gestation may alter cord and serum thyroid hormone homoeostasis.