The preparation, characterization and application of novel anticancer "epirubicin" (EPI) water-compatible magnetic molecularly imprinted polymers (M-MIPs) like artificial antibodies by computational design and chemical synthesis as a carrier for drug delivery is described herein. Two monomers: methacrylic acid (MAA) and methacrylamide (MAM) were selected by computational simulation from the four chemicals used. Covalent and non-covalent bonds were evaluated by this technique based on the interaction mode and energy with template or solvent. Non-covalent bonding was predominant in all cases and major energy interaction was observed. The nanomaterials were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), X-ray powder diffraction (XRD), and a vibrating sample magnetometer (VSM). The loading and controlled release studies performed showed a slight advantage for the M-MIP obtained from MAA than that from MAM at ambient temperature. However, the drug release in vitro was slightly better for the second M-MIP when the temperature increased to 50 °C. The water-compatible nanomaterial showed good pH-sensitive drug release profiles in vitro. Briefly, due to its magnetic property, amphiphilicity, good biomimetic recognition of EPI, high adsorption capacity and controlled release, the epirubicin M-MIPs synthesized in this study are suitable to be applied to a magnetic targeted drug delivery system.