The work focused on manufacturing improved drug loaded multifunctional magnetic nanoparticles that can overcome the relative non-specificity and potential side-effects of some chemotherapeutic drugs to healthy tissues. A new drug delivery system, Chelerythrine (CHE) and Fe3O4 loaded multi-walled carbon nanotubes (Fe3O4/MWNTs-CHE nanocomposites) that can target hepatocytes when treating malignant tumors, was prepared through a simple adsorption method. The formulation and structure of the Fe3O4/MWNTs-CHE nanocomposites were characterized by vibrating sample magnetometer (VSM), Fourier Transform infrared spectroscopy (FTIR) and Scanning Electron Microscopy (SEM). The cytotoxicity and anti-proliferation effect from the prepared nanocomposites were in vitro tested on human hepatocarcinoma HepG2 and normal liver LO2 cell lines. The results showed the saturated magnetization of Fe3O4/MWNTs-CHE nanocomposites could reach to 45.4O3 emu/g, and the in vitro CHE release behavior exhibited a biphasic release pattern. Moreover, the in vitro cytotoxicity studies revealed that the Fe3O4/MWNTs-CHE nanocomposites showed an efficient inhibition rate to HepG2 cell line and exhibited a lower cytotoxicity to LO2 cell line in comparison to the native CHE. Therefore, the multifunctional Fe3O4/MWNTs-CHE nanocomposites should be a useful and promising candidate for treatment of malignant tumors.