Fabrication of an organic polymer nanofiltration membrane with both high water permeability and high salt rejection is still a big challenge. Herein, phytic acid (PhA)-modified graphene oxide (GO) was used as the membrane thickness modifier, which was introduced into the thin-film nanoparticle composite (TFN) membrane via in situ interfacial polymerization (IP) on a porous substrate. The water flux of the optimally tuned TFN-GP-0.2 composite membrane is 48.9 L m-2 h-1, which is 1.3 times that of the pristine thin-film composite (TFC) nanofiltration membrane (37.9 L m-2 h-1) (GP represents the PhA modified GO composite). The rejection rate of 2000 ppm MgSO4 for TFN-GP-0.2 membranes was maintained at 97.5%. The increased water flux of the TFN-GP composite membrane compared to that of the TFN nanofiltration membrane was mainly attributed to enhanced hydrophilicity and reduced thickness of the polyamide (PA) layer. Molecular dynamics (MD) simulations confirm that the diffusion rate of amine monomers is reduced by the presence of a GP complex in the IP process, which facilitates the formation of PA layer with thinner thickness. In addition, the TFN-GP-0.2 composite membrane also showed good long-term stability; after 12 h of continuous operation, the water flux only decreased by 0.1%. This study sheds new light on the development of GO-based nanofiltration for potential implementation, as well as a unique concept for manufacturing high-performance nanofiltration membranes.