In this work, we developed a polymer encapsulation of Fe3O4 nanoparticles as a core-shell nanocluster with different sizes to investigate the cluster structure effect on their magnetic properties and magnetic heating behavior. Well-dispersed nanoclusters of O-carboxymethyl chitosan-coated Fe3O4 nanoparticles were synthesized by microwave-assisted co-precipitation. The cluster sizes were tunable by varying the concentration of polymers used during synthesis. Nanoclusters present superparamagnetic behavior at room temperature with a reduction in saturation magnetization as a consequence of coating layer. The shift of blocking temperature to the higher value with increasing clusters size shows the stronger magnetic interaction in larger magnetic clusters. In a low alternating magnetic field with frequency of 178 Hz and amplitude of 103 Oe, nanoclusters offer a high heating efficiency. A maximum specific absorption rate of 204 W/g is observed in the sample with hydrodynamic size of 53 nm. In vitro cytotoxicity analysis performed on HeLa cells verified that nanoclusters show a good biocompatibility and can be an excellent candidate for applications in hyperthermia cancer treatment.