In this study, preparation, characterization and catalytic application of a novel core–shell structured magnetic with carbon and mesoporous silica shells supported guanidine (Fe3O4@C@MCM41-guanidine) are developed. The Fe3O4@C@MCM41-guanidine was prepared via surfactant directed hydrolysis and condensation of tetraethyl orthosilicate around Fe3O4@C NPs followed by treatment with guanidinium chloride. This nanocomposite was characterized by using Fourier transform infrared spectroscopy, vibrating sample magnetometry, scanning electron microscopy, transmission electron microscopy, energy dispersive X-ray spectroscopy, thermal gravimetric analysis, wide-angle X-ray diffraction and low-angle X-ray diffraction techniques. This nanocomposite have high thermal, chemical stability, and uniform size. Fe3O4@C@MCM41-guanidine catalyst demonstrated high yield (91–98%) to prepare of Knoevenagel derivatives under the solvent free conditions at room temperature in the shortest time. Also, this catalyst was recovered and reused 10 times without significant decrease in efficiency and stability. Fortunately, an excellent level of yield (98–82%) was observed in the 10 consecutive catalyst cycles.