In this study, novel magnetite (Fe3O4)/mesoporous silica nanoparticles (MSN) were prepared by the green synthesis method using Moringa oleifera extract with various MSN concentrations. The crystallite size of Fe3O4/MSN decreased from 10.5 to 9.0 nm with the increase of MSN concentrations. However, as shown from transmission electron microscope images, the surface modification process increases its particle size from 10.7 ± 0.1–27.8 ± 0.3 nm. Scanning electron microscopy images revealed that MSN has a porous structure, and the shape of Fe3O4/MSN was nearly spherical. The Fourier transform infrared spectra showed the functional group of Si-O-Si at 1041 cm−1, indicating a successful surface modification process. After modification using MSN, the band gap energy of the nanoparticles decreased from 3.61 to 3.27 eV. The magnetic properties analysis showed that the saturation magnetization of Fe3O4 and Fe3O4/MSN was 55.32 ± 0.03 emu/g and 53.45 ± 0.04 emu/g, respectively. In contrast, the coercivity increased from 57.7 ± 0.3–149.5 ± 0.5 Oe. Additionally, the specific absorption rate (SAR) of Fe3O4/MSN to evaluate its potential for magnetic hyperthermia applications were investigated. The highest SAR values of Fe3O4 and Fe3O4/MSN were 91.8 mW/g and 86.7 mW/g, which decreased with increasing MSN concentrations. Furthermore, these results proved that the green-synthesized Fe3O4/MSN was a promising candidate and potentially optimized the performance of future magnetic hyperthermia applications.