New monomers have been exploring to fabricate interfacial polymerized thin film composite membranes for decades. N-aminoethyl piperazine (AEP), an aliphatic amine with a heterocyclic structure, was used in this work as an amine monomer to synthesize nanofiltration membranes. Due to the high reactivity nature of AEP, a rate-retarded interfacial polymerization method was applied, which was realized by applying ultra-low AEP concentration (0.07 wt%), low reaction temperature (4 °C monomer solutions), and ice-water quench. The resulting AEP membrane had much better performance (3–4 times permeance and closed rejections) compared with the membranes prepared by the hot water post-treatment and the oven heat treatment. At lower monomer concentrations, an NF membrane with a selective layer thickness of only around 20 nm was prepared by the rate-retarded interfacial polymerization method. The membranes had a negatively charged surface with "willow leaf" like morphology. The MWCO was around 200 g mol−1, and the water permeance was up to 22.8 L m−2 h−1 bar−1, which is comparable with the commercial polyamide membrane NF270. Therefore, AEP is a very competitive alternative monomer for NF membrane synthesis.