We successfully synthesized N-phthaloyl-carboxymethylchitosan (CMPhCh) from chitosan. CMPhCh could be self-assembled to form various morphologies of crew-cut micelle-like aggregates using a mixed solution of water and N,N-dimethylformamide (DMF). The results of scanning electron microscopy, transmission electron microscopy (TEM), and dynamic light scattering (DLS) revealed that the morphologies of the aggregates exhibited vesicles, vesicle-encapsulating vesicles, onion-like vesicles, and large compound micelles (LCM). Their morphologies were changed with varying the concentration of CMPhCh, the ratio of DMF in the mixture, and the self-assembly process. In relatively high CMPhCh concentration and content of DMF, CMPhCh was self-assembled to form the onion-like vesicles with a thin wall and 80-240 nm diameter. For the first time, TEM observation provided straightforward evidence of the onion-like vesicles prepared from natural polymer.