We, herein, describe a novel, simple, efficient and one‐pot multi‐component procedure for the synthesis of substituted pyrimido[4,5‐d]pyrimidines via reaction of N,N‐dimethyl‐6‐amino uracil, isothiocyanate and aromatic aldehydes promoted by 7‐aminonaphthalene‐1,3‐disulfonic acid (ANDSA)‐functionalized magnetic Fe3O4@SiO2 in water as solvent and without using any other harmful organic reagents. Compared with other reactions, using these organic–inorganic hybrid heterogeneous catalysts can help us to achieve a green procedure, high catalytic activity, easy recovery with an external magnetic field, and short reaction times.