In this study, L-cysteine functionalized POSS nanoparticles were synthesized. The synthesized nanoparticles and methyl-methacrylate were applied to fabrication of polyether-imide-thin film nanocomposite nanofiltration membrane. The ratio of (MMA: NPs) changed to obtain efficient separation performances and good antifouling properties. Fourier transform infrared spectroscopy (FTIR), field emission scanning electron microscopy (FESEM), and atomic force microscopy (AFM) analysis were used in membranes characterization. Pure water flux, Na2SO4, CrSO4, Pb(NO3)2 and Cu(NO3)2 rejection, membrane porosity, mean pore size of membrane and water contact angle were studies. Pure water flux measured 14.3 (L/m2.h) for neat membrane whereas that was 11–70.6 for thin-film membranes. Surface hydrophilicity enhanced and roughness, pore size and porosity decreased by increase of MMA:NPs ratio. The highest Na2SO4, CrSO4, Pb (NO3)2 and Cu(NO3)2 rejection observed 84%, 81%, 83% and 79%, at 0.03 wt.% of MMA:NPs ratio. FRR% measured ~95% at 0.03 wt.% of MMA:NPs ratio whereas it was ~29 for neat membrane.