Monomers are elementary units that constitute the polyamide layer, which determines the properties of nanofiltration membranes. The design of nanofiltration membranes with both high separation performance and outstanding chemical stability remains a challenge. In this study, two typical monomers, heterocyclic monomer molecule-piperazine (PIP) and carbon ring molecule-1,4-cyclohexane diamine (CHDA), were applied as aqueous monomers for interfacial polymerization to generate polyamide nanofiltration membranes. The physicochemical properties of the two nanofiltration membranes were comprehensively investigated. The results demonstrated that the nanofiltration membrane fabricated via CHDA exhibited more chemical stability than that fabricated via PIP. The mechanisms influencing the chemical stability difference were elucidated via multiscale simulation. The CHDA polyamide has higher levels of HOMO-LUMO energy and Gibbs-free energy, which make it more stable under harsh chemical environments. Overall, this work presents the effect of the diamine structure on the chemical stability of polyamide NF membranes, which can inspire highly chemically stable nanofiltration membrane fabrication.