In the present study, CuII immobilized on functionalized magnetic mesoporous MCM‐41 (Fe3O4@MCM‐41‐GPTMS‐Gu‐CuII) was prepared as a new, versatile, and magnetically nanocatalyst and characterized by FT‐IR, XRD, small‐angle XRD, BET, TEM, SEM, EDX, EDX‐mapping, TGA, VSM, XPS, and ICP techniques. The characterizations show the presence of MCM‐41 with a hexagonal structure, superparamagnetic behavior, and an average particle size of 8–25 nm. The catalytic activity of the nanocatalyst was evaluated towards the synthesis of structurally different 5‐phenyl‐5,10‐dihydropyrido[2,3‐d : 6,5‐d′]dipyrimidine‐2,4,6,8(1H,3H,7H,9H) tetraone derivatives through one‐pot multicomponent condensation under green conditions. Fe3O4@MCM‐41‐GPTMS‐Gu‐CuII catalyzed many consecutive trials at least five runs. High to excellent yields in short reaction times, simple procedure, environmental friendliness, less toxic solvents, high stability, and reusability of the catalyst are considerable advantages of the prepared catalytic system.