The present invention relates to chitosan nanoparticles for delivering an immunomodulatory agent and a preparation method thereof in aqueous phase. The chitosan nanoparticles were prepared by ionic gelation method, based on inter and intra bonding between positively charged chitosan and negatively charges generating poly anion. The size of nanoparticles is also suitable to target them to M cells of peyer"s patches located in intestinal follicle associated epithelium. The nanoparticles can be used in treating and preventing immunosuppression.