The present invention relates to a conjugate of chitosan and polyamine polymer that is useful for transferring a desired gene medicine into cells, and a method for preparing the same. In particular, the present invention relates to a double conjugate that is prepared by 1 in king poly-L-arginine to low molecular weight chitosan or triple conjugate that is prepared by additionally linking polyethylene glycol (PEG) to the double conjugate, and a method for preparing the same. The chitosan based cationic polymer conjugate of the present invention forms a complex with negatively charged gene medicine such as plasmid DNA and small interfering RNA to efficiently transfer the desired gene medicine into cells with low cytotoxicity. Accordingly, the conjugate can be used as an effective delivery system for in vivo administration of gene medicine.