Ionic liquid functional MCM-41 was synthesized, characterized and used as heterogeneous catalyst for the Knoevenagel condensation of isatins with malononitrile. A series of corresponding isatylidene malononitrile were obtained in high isolated yield (96–99%) at room temperature in a short time. The heterogeneous catalyst can be easily recovered by centrifugation and showed almost no loss of activity over 10 recycle experiments. At the same time, the gram-scale experiments showed excellent yields and provided a highly effective method for scale up applications.