The present invention provides a method for fabricating a semiconductor structure. A multilayer structure on is formed a substrate, the multilayer structure includes at least a first dielectric layer, a second dielectric layer and an amorphous silicon layer, next, a first etching step is performed, to forma first recess in the amorphous silicon layer and in the second dielectric layer, parts of the first dielectric layer is exposed by the first recess, afterwards, a hard mask layer is formed in the first recess, a second etching step is then performed to remove the hard mask layer and to expose a surface of the first dielectric layer, and a third etching step is performed with the remaining hard mask layer, to remove a portion of the first dielectric layer, so as to form a second recess in the first dielectric layer.