Rejection of endocrine-disrupting compounds (EDCs) by thin-film composite (TFC) polyamide membranes remains a challenging issue in wastewater reclamation applications because of the unfavorable hydrophobic interaction between EDCs and membranes. Herein, we investigated the incorporation of hydrophilic metal organic frameworks (MOFs) into the polyamide layer to create water/EDC selective nanochannels for enhancing EDC rejection. Using MIL-101(Cr) MOF as a nanofiller, the water flux of the MOF0.20 TFC membrane (0.20 wt/v % MOF in n-hexane) was 2.3 times that of the control. The rejection rates against EDCs involving methylparaben, propylparaben, benzylparaben, and bisphenol A (BPA) by MOF0.20 were also significantly higher than the respective values of the control membrane, with the water/EDC selectivity (e.g., A/BBPA) of MOF0.20 approximately doubled compared to that of the control. Further single salt rejection and gold nanoparticle filtration tests confirmed that the hydrophilic nanochannels created by MOFs played a critical role in membrane transport, accounting for the significant enhancement of EDC rejection of the modified TFC membrane. This study demonstrates a promising membrane modification protocol using hydrophilic MOFs for achieving selective removal of EDCs and high-efficient wastewater reclamation using TFC membranes.