Polyamide (PA) reverse osmosis membranes are commonly employed in seawater desalination owing to their effective salt rejection and water permeability; however, the elimination of small and neutral boron molecules from seawater remains a significant hurdle in energy-efficient and cost-effective desalination processes. In this work, a seawater reverse osmosis (SWRO) membrane with powerful boron removal competence was designed by adopting an in-situ rapid integration protocol, which utilized aliphatic amines as hydrophobic barriers by bonding the residual chloride groups upon the membrane surface and as molecular plugs by embedding in the PA networks. Consequently, it resulted in a notable improvement in the rejection of neutral boron molecules due to enhanced steric hindrance caused by immobilized amine plugs and synergistically tunned hydrophobic interactions. The permeability coefficient of boron decreased from 4.8 to 0.9 L m−2 h−1, and the boron rejection increased from 80.7 to 90.5% under the modification conditions with the optimal type and concentration of amines, while displaying a NaCl rejection of 99.8% and an acceptable water permeability of 0.55 L m−2 h−1 bar−1. Meanwhile, the alteration of membrane chemical compositions and structure properties was kept to a minimum. This study offers intuitive insights into the critical roles played by the aliphatic amines in the selective layer of the membrane for the removal of neutral boron molecules and salts, thereby enabling the fabrication of highly selective SWRO membranes, which may have significant implications for more efficient membrane-based seawater desalination and boron removal.