The application of reverse osmosis (RO) is restricted with scaling and organic fouling problems. In this work, we reported a series of RO membranes with excellent anti-scaling and anti-fouling properties, which were fabricated through post-modification with small molecules consisting of sulfonate or phosphate groups, including L-O-Phosphoserine (L-SOP), 3-Amino-1-propanesulfonic acid (APSA) and Alendronate sodium trihydrate (AS). Detailed characterizations of modified membranes were carried out, indicating that the modified membranes had smoother surface, better hydrophilic properties and more negatively charged surface. More importantly, after simulated scaling and fouling experiments, the modified membranes exhibited lower flux decline rates and higher flux recovery ratios. The mechanisms for anti-scaling and anti-fouling properties were analyzed. The modified membranes would have promising application due to its easy-to-operate method and excellent scaling and fouling resistances.