In this study, to obtain low molecular water soluble chitosan(LMWSC) with various molecular weights, the crude chitosan oligosaccharides (COS) was separated according to its molecular weight by using ultrafiltration technique. LMWSC with a free amine group was prepared by the novel salts-removal method. The characterization of fractioned LMWSC and degree of deacetylation (DDA) were identified by FT-IR and 1H-NMR spectra. At the GPC measurement, molecular weight of fractioned LMWSC to 1~3K, 3~10K, 10~30K were 3900, 7400, 12800, respectively. To identify potential as a gene carriers, Successfully fractioned COS and salt-removed LMWSC confirmed transfection efficiency using 293T cell.