Magnetic alpha-Fe2O3-MCM-41 mesoporous material functionalized by dual acidic ionic liquid (DAIL) was prepared through a two-step approach as a novel powerful acidic catalyst which provides high ionic media for reactions, by means of post-surface grafting of the mesochannels of alpha-Fe2O3-MCM-41 materials with 3-sulfobutyl-1-(3-propyltrimethoxysilane)imidazolium hydrogen sulfate as DAIL. Mesoporous MCM-41 was simply packed on the surface of ferric oxide nanoparticles and DAIL was efficiently incorporated into the mesochannels of MCM-41 generating Lewis and Bronsted acidic sites. The catalyst was characterized by FT-IR, X-ray powder diffraction, HRTEM, vibrating sample magnetometer, X-ray energy diffraction spectra, thermogravimetric and differential thermal analyses, and N-2 adsorption-desorption measurements. The synthesized hybrid acidic MCM-41 showed good catalytic performance in the one-pot synthesis of pyrimido[4,5-d]pyrimidine derivatives using 6-aminouracil, aldehyde, and urea or thiourea under solvent free conditions. Moreover, it was proved that under this condition, the use of such a hybrid material as a catalyst plays the role of rendering the reactions while neither the alpha-Fe2O3-MCM-41 nor the 3-methyl-1-(4-sulfonic acid)butylimidazolium hydrogen sulfate were able to promote this reaction.