Polyamide (PA) membranes prepared by interfacial polymerization (IP) provide an effective solution for efficient desalination. The IP reaction, as a diffusion-controlled polymerization reaction, regulates the storage and diffusion of monomers in the IP process to achieve effective regulation of the PA membrane structure. Higher initial monomer concentration and slower monomer release rate can effectively reduce the membrane thickness and enhance the permeance of the membrane. Herein, ionic covalent organic framework (iCOF) materials with well-developed and ordered pore channels bearing high-density –SO3H groups are used to construct a porous and charged interlayer to regulate the release process of monomers during the IP process. The well-ordered pore structure of iCOF provides sufficient storage space for amine monomers and uniform monomer distribution, accelerating the closure of the incipient film. Moreover, the electrostatic interactions between the high density of negatively charged anionic groups on iCOF and the positively charged amine monomer can reduce the diffusion coefficient of the amine monomer by a factor of two. The above two effects resulted in a nearly 10-fold reduction in the thickness of the PA separation layer and an increase in water permeance up to 24.8 L m−2 h−1 bar−1, nearly three times improvement compared to unmodified PA membrane.