Zwitterions have been attracting great attention for researchers to tailor the separation membranes featuring enhanced water permeability and excellent antifouling property. Here we functionalized polyamide membrane surface with small-molecule zwitterions through sequential interfacial polymerization (SIP) technique to improve the performance of RO membranes. Zwitterionic molecules 3-(4-(2-((4-aminophenyl)amino)ethyl)morpholino-4-ium)propane-1-sulfonate (PPD-MEPS) and amino acid arginine were covalently bonded onto the PA surface via the amine groups of two zwitterions. Consequently, the surface hydrophilicity of both modified membranes were significantly improved with WCA decreased from ~60° to ~28°, and their surface negative charge also decreased to some extent at high pH values. The water permeability increased from 2.45 LMH/bar to 3.81–3.85 LMH/bar, increasing by about 57%, while maintained a NaCl rejection as high as 98.5%. In addition, the zwitterions-modified RO membranes exhibited much improved antibacterial attachment (E.coil) and fouling resistance to model foulants bovine serum albumin (BSA), lysozyme (LYZ) and humic acid (HA). Therefore, the facile zwitterions modified membranes possessing high water permeability and excellent antifouling performance, especially using amino acid Arg may find their potential promising application in water treatment.