In this research L-cysteine as an amino acid was applied to modification of octa glycidyloxypropyl-silsesquioxane (glycidyl POSS) and construction of L-cysteine modified-POSS nanoparticles. The synthesized nanoparticles were introduced into PEI-based nanofiltration membranes for tuning of membrane permeability, antifouling ability and separation efficiency. Fourier transform infrared spectroscopy (FTIR), field emission scanning electron microscopy (FESEM), X-Ray diffraction analysis (XRD) and atomic force microscopy (AFM) analysis were used for characterization of synthesized nanoparticles and prepared membranes. The membranes porosity, mean pore size, contact angle, water content, pure water flux, Na2SO4 and CrSO4 rejection and antifouling properties of membranes also studied. The results showed that pure water flux (PWF) enhanced from 17.63 L/m2 h for neat membrane to 95 L/m2 h for the blended 1 wt% [L-cysteine-co-POSS/PEI] membrane. The Na+ and Cr+2 rejection measured 69% and 52% for pristine PEI membrane whereas they were 80% and 79% for the modified membrane containing of 1 wt% nanoparticles. The highest FRR% was also obtained 95% for the blended [1 wt% NPs-PEI] membrane.