Monodispersed MnxZn1-xFe2O4 magnetic nanoparticles of 8 nm are synthesized and encapsulated in amphiphilic block copolymer for development of the hydrophilic magnetic nanoclusters (MNCs). These MNCs exhibit superparamagnetic characteristics, high specific absorption rate (SAR), large saturation magnetization (Ms), excellent stability, and good biocompatibility. MnFe2O4 and Mn0.6Zn0.4Fe2O4 are selected as optimum compositions for the MNCs (MnFe2O4/MNC and Mn0.6Zn0.4Fe2O4/MNC) and employed for magnetic fluid hyperthermia (MFH) in vitro. To ensure biosafety of MFH, the parameters of alternating magnetic field (AMF) and exposure time are optimized with low frequency, f, and strength of applied magnetic field, Happlied. Under optimized conditions, MFH of MnFe2O4/MNC and Mn0.6Zn0.4Fe2O4/MNC result in cancer cell death rate up to 90% within 15 min. The pathway of cancer cell death is identified as apoptosis, which occurs in mild hyperthermia near 43 °C. Both MnFe2O4/MNC and Mn0.6Zn0.4Fe2O4/MNC show similar efficiencies on drug-sensitive and drug-resistant cancer cells. On the basis of these findings, those MnxZn1-xFe2O4 nanoclusters can serve as a promising candidate for effective targeting, diagnosis, and therapy of cancers. The multimodal cancer treatment is also possible as amphiphilic block copolymer can encapsulate, in a similar fashion, different nanoparticles, hydrophobic drugs, and other functional molecules.