Limited studies have consistently shown an association of phthalates exposure with thyroid hormones (THs) in pregnant women. However, it remains unknown on which specific phthalates can affect THs and whether any effects could differ by gestational age. In the present study, we investigated associations between serum concentrations of phthalate monoesters [monoethyl phthalate (MEP), mono-(n + iso)-butyl phthalate (MBP) and mono(2-ethylhexyl) phthalate (MEHP)] and THs [thyroid-stimulating hormone (TSH), total thyroxine (TT4) and free thyroxine (FT4)] in Chinese pregnant women. 1,397 women were recruited from the China-Anhui Birth Cohort. Maternal serum samples were collected and used to measure phthalate metabolites and THs. Covariate-adjusted linear regression analyses showed that natural log (Ln)-transferred concentrations of MBP and LnMEHP were negatively associated with TT4 (β = -0.277 and -0.461, respectively; p < 0.001). Stratification analyses by gestational weeks showed significant associations of LnMBP and LnMEHP with TT4 in gestational weeks 5 to 8, 9 to 12, and 13 to 20. Our findings suggest an association of serum phthalates with lower TT4. The influence of MBP and MEHP on TT4 concentrations throughout the early pregnancy may begin from the embryonic stage (gestational weeks 5 to 8).