As a promising technology for lithium extraction from salt lakes, nanofiltration membranes still face challenges in balancing between permeability and selectivity. In this paper, highly dispersed functionalized boron nitride nanosheets (BNNSs-NH2) were prepared by modifying exfoliated boron nitride nanosheets (BNNSs) with polydopamine, which were incorporated into a polyamide (PA) layer by aqueous phase conditioning to prepare positively charged polyamide nanofiltration membranes. Scanning electron microscopy (SEM) showed that the PDA nanoclusters on the surface of the BNNSs can disrupt the regular stacking parallel to the membrane surface. Energy spectrum (EDS) of SEM and X-ray photoelectron spectroscopy (XPS) etching further revealed that BNNSs-NH2 were dispersed within PA layer, creating transmembrane channels for molecular diffusion. The results showed a pure water permeance of 8.55 ± 0.24 L/m2 h bar, indicating that the stabilized intercalation of BNNSs-NH2 in the PA layer synergistically improved the water permeability. Meanwhile, the retention rate of MgCl2 remained at 94 %, which was attributed to the enhanced compatibility between BNNSs-NH2 and polyamide matrix by the polydopamine coating (PDA) on the surface, as well as the Dornan effect repulsion by the enhanced positive charge on the membrane surface. After the three-stage nanofiltration of membrane, the Mg2+/Li+ ratio decreased from 50 to 0.12. Overall, this method balances permeability and selectivity by adjusting pore size and positive charge, potentially offering new ideas and insights for the preparation and development of nanofiltration membranes for Mg2+/Li+ separation.