Cationic cetyltrimethylammonium (CTAB) is an effective and common intercalator for interlayered modification in layered materials, while its biotoxicity remains an issue. To improve biosafety and biocompatibility of the drug delivery system, the nontoxic chitosan (CS) was introduced into CTAB‐modified kanemite (Ka‐CTAB). Accordingly, the obtained Ka‐CTAB/CS was further used as a drug carrier of methotrexate (MTX). Various characterizations were employed to investigate the drug delivery system based on the Ka‐CTAB/CS. Results revealed that the loading capacity of the drug delivery system based on the Ka‐CTAB/CS for MTX was about 13.47%, and the drug delivery system exhibited slow and sustained release of drugs either in phosphate buffer solution (pH = 7.4) or in HCl solution (pH = 1.35). The introduction of CS in Ka‐CTAB/CS not only replaced a part of CTAB in composition but also prevented CTAB molecules falling off the carrier during the drug‐releasing process. In the methyl orange dye assay, the concentration of free CTAB shed from Ka‐CTAB/CS was as low as 8.09 × 10−7 mol/L after 24 h. In an in vitro cell viability assay using HepG2 cells, Ka‐CTAB/CS also exhibited lower cytotoxicity compared to previous Ka‐CTAB.