The present invention relates to an anticancer drug-chitosan complex forming self-aggregates and the preparation method thereof. More precisely, the present invention relates to the anticancer drug-chitosan complex forming self-aggregates in aqueous media composed of a hydrophobic anticancer agent and a hydrophilic chitosan, and the preparation method thereof. The anticancer drug-chitosan complex of the present invention not only works selectively against target tumor tissue but also continues to release the medicine over a long period of time. Besides, the anticancer drug-chitosan complex could have greater amount of drug by adding the anticancer drug into self-aggregates, which is generally limited by chemical bond. Therefore, the anticancer drug-chitosan complex of the present invention can be effectively used for the cancer chemotherapy.