Starch nanoparticles were produced by dialysis method from octenyl succinic anhydre (OSA) and 1,4-butane sultone (BS). The properties of the self-assembled nanoparticles were characterized by NMR spectroscopy (DOSY), fluorescence spectroscopy and dynamic light scattering (DLS). In order to investigate the formation of hydrophobic microdomains, the Nile Red dye was used as a fluorescent probe to evaluate the critical aggregation concentration (CAC) of modified starch in aqueous solution. The results show that the entrapment of the molecular guest was effective and only restricted by the solubility limit of the starch. Then, the modified starch was applied to solubilize benzo[a]pyrene (BaP) in view of degradation by Fenton process. Finally, it has been shown that 95% of BaP was degraded when it was encapsulated in OSA-BS-starch nanoparticles.