• PIP has been applied as a structure regulator to enlarge pores of PA NF membranes. • The addition of PIP enhances the permeance by 97.3% with rejection of MO above 98%. • TPC has been deployed for narrowing pore size distribution of the PA NF membranes. • The incorporation of TPC enhances rejection to positive multi-valent ions greatly. • The finely tailored membranes show strong promise in waste water treatment. With fine pore structures and abundant surface charge, polyamide nanofiltration membranes have been widely deployed for separating small active organic molecules and multi-valent ions. However, lack of highly permeable membranes with excellent rejection towards target molecules hampers the widespread application of the polyamide (PA) nanofiltration membranes on a large scale. In current study, we conceive a facile strategy to regulate the molecular structure of polyamide selective layer through introducing piperazine (PIP) or terephthaloyl chloride (TPC) as a structural regulator during the interfacial polymerization between polyethyleneimine (PEI) and trimesoyl chloride (TMC). On the one hand, adding PIP to aqueous solution enlarges the length between the crosslinked networks, thereby enhancing the pure water permeance by 97.3% (to 23.70 L m −2 h −1 bar −1 ). Interestingly, the membranes exhibit excellent performance for dyes separation (rejection greater than 98%) and molecular weight cut-off (MWCO) about 554.34 Da under the optimum separation conditions. On the other hand, the introduction of TPC could assist the formation of crosslinked structures, thereby narrowing the pore size distribution of the membranes. The well-designed membranes reject above 98% PbCl 2 with permeance about 6.36 L m −2 h −1 bar −1 and MWCO below 150 Da under the optimum operation conditions, which is preferable to the state-of-art PA membranes. Excitingly, all of the well-designed membranes demonstrate excellent anti-fouling performances. In summary, with finely tailored pore structure, high permeance and high rejection, and excellent anti-fouling performance, the obtained membranes show strong promise in treating effluence from printing and dyeing industry, and metallurgy and mining industry, respectively.