The rapid development of modern industrialization has put forward high demands on separation and purification technologies. To reduce energy consumption, improve efficiency, and enhance process flexibility, nanofiltration membranes for high temperature separation have become more and more important. Herein, we report the use of 3,3′-diaminobenzidine (DAB) as the aqueous phase monomer and trimesoyl chloride (TMC) as the organic phase monomer to engineer thermally resistant nanofiltration membranes via interfacial polymerization. The incorporation of DAB enhances the rigidity of the cross-linked polyamide network, reduces segmental thermal motion at high temperature, and improves the thermal stability of the composite membrane. The variations in fractional free volumes of the nanofiltration membranes were analyzed at different temperatures by molecular dynamics (MD) simulation, which have also been confirmed by experiments. The findings reveal that incorporating a rigid monomer into the polyamide layer can significantly enhance the thermal resistance. The resultant composite membrane exhibits outstanding resistance to high-temperature feed solutions, boasting a highly stable rejection rate (97.0 %) to Na2SO4 between 25–85 °C. Remarkably, even under sustained operation at 85 °C for 12 h, the rejection rate is consistently stable. This work presents a novel system for the design of thermally stable nanofiltration membranes for high temperature separation.