Microporous organic nanotubes (MONs) hold considerable promise for designing molecular-sieving membranes because of their high microporosity, customizable chemical functionalities, and favorable polymer affinity. Herein, we report the use of MONs derived from covalent organic frameworks to engineer 15-nm-thick microporous membranes via interfacial polymerization (IP). The incorporation of a highly porous and interpenetrated MON layer on the membrane before the IP reaction leads to the formation of polyamide membranes with Turing structure, enhanced microporosity, and reduced thickness. The MON-modified membranes achieve a remarkable water permeability of 41.7 L m⁻² h⁻¹ bar⁻¹ and high retention of boron (78.0%) and phosphorus (96.8%) at alkaline conditions (pH 10), surpassing those of reported nanofiltration membranes. Molecular simulations reveal that introducing the MONs not only reduces the amine molecule diffusion toward the organic phase boundary but also increases membrane porosity and the density of water molecules around the membrane pores. This MON-regulated IP strategy provides guidelines for creating high-permeability membranes for precise nanofiltration.