In recent years, the global demand for lithium resources has grown substantially due to the rapid development of the new energy industry. The nanofiltration (NF) technique is a feasible method to extract lithium from salt-lake brine, and the high Mg2+/Li+ separation selectivity of the NF membrane is the crucial factor in the NF separation process. In this work, the polyamide (PA) layer was prepared on the polyphenol/PEI interlayer-modified polysulfone (PSF) substrate to endow the NF membrane with decreased pore size and weakened electronegativity. Enhanced steric hindrance effect and reduced electrostatic attraction between Mg2+ and PA layer increased the Mg2+ rejection, thereby improving the Mg2+/Li+ separation factor of the NF membrane. Furthermore, the positively charged polyphenol/PEI interlayer hindered the permeation of Mg2+ through the Donnan effect, further enhancing the Mg2+/Li + separation factor. A separation factor up to 50.7 for Mg2+/Li+ was achieved by extracting lithium from simulated brine using the obtained NF membrane. In addition, the NF membrane exhibited a permeability of 18.6 L m−2 h−1·bar−1 and excellent long-term stability, which greatly improved the Mg2+/Li+ separation efficiency and reduced energy consumption. Therefore, this work provides a simple strategy for preparing NF membranes with high Mg2+/Li+ separation factor and permeability.