Objective: We investigated whether maternal-biological paternal urinary phthalate metabolites measured during pregnancy were associated with the thyroid hormones of newborns. Methods: This prospective cohort study included 73 pregnant women-newborn-biological father pairs recruited between March 2013 and July 2017. The urine samples from mother-father pairs were collected for 16 phthalates analysis before delivery by liquid chromatography-electrospray ionization mass spectrometry (LC-MS/MS). TSH, free T4, and total T3 were measured in cord serum at delivery. We used multivariable linear regression to assess associations between individual urinary phthalate metabolites and level of cord serum thyroid hormones. Results: The mean ages of female and male partners were 32 and 34 years, respectively. Their gestational age ranged from 30.6-41.0 weeks and 60.3% (n=44) of the infants were male. The mean maternal phthalate levels were significantly higher than the paternal. Significant correlations were observed for several pairs of phthalates (MEHP, 5cx-MEPP, MnBP, DEHP-2, DEHP-4, and DEHP-5) in maternal and paternal urine, suggesting married couple share exposure routes. Multiple linear regression models after adjustments showed positive associations between free T4 of cord blood and maternal MEHP, MEOHP, 5cx-MEPP, DEHP-4, and DEHP-5. Furthermore, negative associations were shown between log TSH and maternal MEOHP, DEHP-3, and DEHP-4. Positive correlations were also shown between free T4 and maternal MEHP, MEOHP, 5cx-MEPP, DEHP-2, DEHP-3, DEHP-4, and DEHP-5 in boys (n=44). However, negative associations were shown in paternal phthalates between free T4 of cord blood and paternal MMP and total T3 and paternal 5cx-MEPP, DEHP-2, and DEHP-5. Conclusion: Our results suggest phthalates were positively associated with freeT4 and log TSH in newborns in this cohort. However, paternal phthalates were inversely associated with free T4 and total T3. Phthalates exposure in utero may adversely affect newborn\'s thyroid hormones.