Water pollution by organic dyes has been one of the great challenges in recent days. The application of nanostructure and nanocatalyst for the degradation of organic dyes is a very effective and useful method for the treatment of water and industrial wastewater. In this research, Fe3O4/rGO/SiO2 dark catalyst nanomaterial was used to remove methylene blue dye from aqueous media. The Fe3O4/rGO/SiO2 nanocatalyst was prepared by an ultrasonic probe approach. The physical, chemical, and morphology properties of synthesized Fe3O4/rGO/SiO2 nanocomposites were investigated by transmission electron microscopy (TEM), energy X-ray dispersion (EDS), Fourier Transform infrared (FT-IR), vibrating sample magnetometer (VSM), Raman, field emission scanning electron microscopy (FESEM), and X-ray diffraction (XRD) analysis. XRD, FT-IR, and Raman analysis results confirmed the successful formation of Fe3O4/rGO/SiO2 structure. VSM analysis results showed that Fe3O4/rGO/SiO2 nanocomposites had good superparamagnetic behavior with a magnetization saturation of 40 emu/g. TEM and FESEM results showed that SiO2 and Fe3O4 were grown on rGO nanosheets, spherically. The Fe3O4/rGO/SiO2 nanocomposites had excellent catalyst activity and methylene blue dye completely degraded in 4 min. The radical scavenger experiment and Zeta potential analysis confirmed that surface electrons of Fe3O4/rGO/SiO2 nanocomposites had an essential role in the dark catalyst activity of Fe3O4/rGO/SiO2 nanocomposite. The experimental results confirmed that Fe3O4/rGO/SiO2 magnetic nanocomposites have good potential to be used as a recyclable and high-performance nanocatalyst for the treatment of water from methylene blue dye.