BPA, a typical endocrine disruptor, poses a significant threat to the growth of crops and thereby jeopardizes sustainable agriculture products and human health. In this work, a water-stabilized imine covalent organic framework (TpBD-COF) packed nanochannel membrane was constructed. The TpBD-COF membrane achieves high selective removal of BPA attributed to the subdivision of the pores by the filled COF, which further reduces the porous size and effectively eliminates the distance barrier between the selective sites of TpBD-COF membranes and BPA. The selective removal ratio of BPA was 5.79 times higher than that of the bare membrane, while the removal capacity reached 6.78 nM cm-2 min-1. It can eliminate BPA from irrigation wastewater and ensure crop growth. The application of COF-filled nanoporous membrane provides not only a size-matching strategy for the development of specific continuous removal of BPA but also a theoretical reference for membrane removal of other organic pollutants in agricultural irrigation water environment.