In this study, magnetite nanoparticles (Fe3O4) were synthesized as a magnetic core by chemical co-precipitation process and coated with a silica layer. The (Fe3O4@SiO2) core-shell magnetic nanoparticles were functionalized by organic-base tags to produce the MNPs-TBAN nanoparticles as a novel hybrid nanostructure. The morphology, stability, and magnetism of this hybrid nanostructure were characterized and studied by Fourier transform infrared spectroscopy (FT-IR), thermal gravimetric analysis (TGA), vibrating sample magnetometry (VSM), X-ray powder diffraction analysis (XRD), scanning electron microscopy (FE-SEM), and transmission electron microscopy (TEM). The prepared hybrid nanomaterial was successfully used as a basic heterogeneous catalyst for the synthesis of pyrano[2,3-d]pyrimidine derivatives, via the condensation of an aldehyde, malononitrile and barbituric acid or thiobarbituric acid. The reaction was afforded the desired products in high purity and has advantages of excellent yields, simple workup procedure, and short reaction time. The catalyst was easily separated from the reaction mixture with the assistance of an external magnet and reused for several runs without noticeable deterioration in catalytic activity.