Extraction of lithium resources from salt lake brines is an effective method to solve the shortage of lithium resources nowadays. However, magnesium-lithium separation has become a critical issue for lithium extraction from salt lakes with high Mg2+/Li+ ratio, due to the similar ionic characteristics of Li+ (0.38 nm), and Mg2+ (0.43 nm). Herein, an amine monomer containing crown ether group (4′-aminobenzo-15-crown-5-ether (NH2–B15C5)) was introduced into the interfacial polymerization (IP) process of piperazine (PIP) and homotrimethylene tricarbonyl chloride (TMC) to prepare polyamide (PA) nanofiltration (NF) membranes with Li+ selective transport channels. NH2–B15C5 shows good compatibility and selective complexation to Li+, which acts as Li+ selective transport channels effectively retaining Mg2+ and allowing Li+ to cross the membrane smoothly, therefore solving the problem of poor lithium-magnesium separation performance of most of the NF membranes currently. Molecular dynamics simulations (MD) also confirmed that NH2–B15C5 has a stronger affinity for Li+ than for Mg2+. The NH2–B15C5/PIP-TMC membrane exhibited excellent separation performance and water permeance in simulated salt lake brine (2000 ppm, WMg/Li = 100), where the SLi, Mg and water permeance were 32.2 and 8.22 L·m−2·h−1·bar−1. Importantly, the crown ether is introduced into the PA separator layer in the form of covalent bonds, hence showing excellent stability. Overall, an NF membrane with high lithium-magnesium separation performance was designed for the extraction of lithium resources from high Mg2+/Li+ ratio salt lake brine.