Polyethyleneimine (PEI) nanofiltration (NF) membranes demonstrate remarkable effectiveness in separating lithium and magnesium from salt lakes, attributed to their positively charged surface. However, undesired permeability resulting from densely cross-linked structures limits the further industrial applications and development of PEI NF membranes. Herein, a high permeable Mg2+/Li+ separation NF membrane with stronger internal and surface positive charge was fabricated using 1-Aminopyridinium iodide (1-AI) for the first time through a capping-grafting synergistic strategy. On the one hand, the monoamine character of 1-AI can realize the end-capping (EC) effect on the acyl chloride monomers in the interfacial polymerization process, which can contribute to a reduction in the cross-linking degree of the membrane. On the other hand, 1-AI with a quaternary ammonium group as the surface grafting (SG) agent can significantly improve the surface positive charge property of the membrane. The synergistic effect of capping-grafting not only rendered the membrane looser and effectively enhanced the surface positive charge of the membrane, but also increased the depth of grafting modification, leading to a notable rise in the internal positive charge of the membrane. After the capping-grafting treatment, the water permeance of the PEI-EC/SG membrane reached 19.8 L·m−2·h−1·bar−1, approximately 4.5 times that of the original PEI membrane, while keeping an ideal MgCl2 rejection rate (97.1%) and exhibiting good Mg2+/Li+ selectivity (27.7). This work demonstrates the advantages of the capping-grafting synergistic method in regulating membrane structure for improving permeability as well as the surface and internal charge properties of the membrane for enhancing ion selectivity.