Polyamide (PA) nanofiltration (NF) membranes with excellent permeability and selectivity have always been the ultimate pursuit of desalination technology. Herein, we present a guanidinium manipulated interfacial polymerization strategy to develop guanidyl-integrated PA NF membranes with ultra-high permselectivity. A nylon microfiltration membrane is utilized as the support to conduct spatial-temporal regulation of amine monomers along with controllable diffusion reaction. Through introducing 1,3-diaminoguanidine (DAG) or triaminoguanidine (TAG) into the aqueous piperazine solution, the free volumes of PA membranes could be well modulated at the sub-angstrom scale. Consequently, the TAG-integrated PA membrane exhibited high water permeance of 33.1 LMH bar−1 and superior Na2SO4 rejection of 99.2%. Meanwhile, this membrane achieved outstanding anion sieving capability (Cl−/SO42− ∼ 343) and nearly 100% tetracycline removal, which is superior to the “state-of-the-art” PA NF membranes. The DAG-integrated PA membrane attained ultra-high water permeance of 46.5 LMH bar−1 due to its relatively large free volume. In addition, the nylon composite PA membranes displayed desirable anti-pressure and organic solvent-resistant abilities. This study provides a convenient and scalable preparation strategy for highly permselective NF membranes, which holds great application potential in desalination and resource recovery.