Developing an effective and stable separation membrane for water treatment is of much interest while challenging because of the restrictions of membrane fouling and water flux reduction. To minimize this problem, in this work, highly porous and hydrophilic nanostructure of NH₂-modified MCM-41 (NH₂-MCM-41) was embedded successfully into the nanofiltration (NF) membrane body via commonly used phase inversion method. The unmodified and modified nanofiller was analyzed by Fourier Transform Infrared (FTIR) spectroscopy, X-Ray powder diffractometry (XRD), field emission scanning electron microscopy (FE-SEM), thermogravimetric analysis (TGA), and nitrogen adsorption–desorption. Furthermore, the modified membranes were characterized through surface and cross section FE-SEM images, the membrane surface roughness, hydrophilicity, antifouling properties and dye rejection. Benefiting from porous networks and enhanced hydrophilicity, the mixed matrix membranes (MMMs) revealed more prominent hydrophilic property as well as higher pure water flux (PWF) compared with naked membrane. The polysulphone (PSf) membrane modified with NH₂-MCM-41-1.0 exhibited the highest pure water flux (PWF) of 65.43 kg/m².h and superior antifouling characteristics with a flux recovery ratio (FRR) of around 97.0% and an irreversible fouling resistance (R_ir) of 3.2%. Furthermore, the optimal membrane possessed high dye rejection (100%) and antifouling capacity (FRR of 97%) while filtering a field sample, effluent from a local stabilization pond treating municipal wastewater. The fabricated membrane in this study is believed to pave pathways for constructing NF membranes with superior effectiveness for other municipal and industrial wastewaters treatment.