Through molecular simulations and density functional theory, we explored a novel approach leveraging molecular engineering-tuned pore chemistry to create active pores in polyamide membranes, enabling exceptionally high-efficiency selective removal of neutral molecules such as boric acid from water. This approach aims to achieve supremely high-efficiency selective water-boric acid separation without sacrificing water permeation efficiency, delivering up to a 20-fold enhancement in selectivity along with a significant improvement in water permeance. To elucidate the underlying mechanism behind such exceptional efficiency, we systematically analyzed the transport properties of water and boric acid across polyamide membranes with pore chemistry precisely tailored through molecular engineering. Our simulations highlighted the pivotal role of pore chemical characteristics in governing molecular selective separation behavior. Specifically, the pore walls in polyamide membranes, characterized by enhanced electronegative attributes, effectively regulate water-membrane-boric acid interactions, diffusion behavior, and migration barriers, enabling efficient selective transport while maintaining high water permeance. These investigations provide molecular-level insights that inform the design and fabrication of next-generation high-performance polymer membranes with pore-chemistry-modulated properties for the separation of small neutral molecules.