Endowed with designable pore structure and intrinsically interconnected channels, metal-organic frameworks (MOFs) offer immense potential as functional nanofillers to boost the performance of nanocomposite membranes. However, achieving optimal pore size matching between MOFs and the polymer matrix while maintaining robust interfacial affinity remains a significant challenge in fabricating high-performance nanocomposite membranes. Herein, natural organic polyphosphate phytic acid was utilized to functionalize PCN-224 to narrow its pore size and enhance the polymer affinity. Thin-film nanocomposites containing mPCN-224 were afterward synthesized on the polysulfone support through a combined approach of anodic electrophoretic deposition (EPD) and vacuum filtration-assisted interfacial polymerization (VF-IP). The incorporation of mPCN-224 nanoparticles not only enhanced the hydrophilicity and electronegativity of the polyamide film but also led to a substantial reduction in film thickness. This is likely attributed to lessened piperazine supply at the interface, related to its limited diffusion at the presence of negatively charged mPCN-224. The additional nanochannels provided by mPCN-224, coupled with the loose PA layer, resulted in a substantial 56.3 % increase in the water permeance of the TFN-mPCN-224 membrane, reaching 20.0 L m−2 h−1 bar−1. Additionally, the post-synthesis modification with phytic acid led to an improved Cl−/SO42− selectivity coefficient of 44, substantially higher than that of the TFN-PCN-224 membrane. This improvement was primarily attributed to the narrowed pore size of mPCN-224 and the enhanced surface electronegativity. This study introduces a pathway for developing high-performance TFN membranes based on post-synthetic modification of MOF nanofillers with phytic acid molecules.