A method of forming a self-aligned contact via for a MRAM is disclosed. A first conductive layer, a pinned layer, a tunneling barrier layer, a free layer, a capping layer and a first dielectric layer are formed sequentially over a substrate has formed lots of transistors and interconects. A portion of the first dielectric layer and the capping layer are removed until a surface of the free layer is exposed. A portion of the pinned layer, the tunneling barrier layer and the free layer are removed to form a MRAM device. A second dielectric layer is formed over the magnetic random access memory device. A planarization process is performed to form a planar surface of the second dielectric layer. The first dielectric layer and a portion of the second dielectric layer are removed to form a self-aligned contact opening. A second conductive layer is filled into the self-aligned contact opening.