A method for fabricating a semiconductor structure with a multi-layer storage capacitor is provided. A substrate having an active element area and a storage capacitor area is provided. By sequentially fabricating a semiconductor layer, a first inter-layer dielectric (ILD) layer, a gate and a first electrode, a source and a drain in the semiconductor layer in the active element area, a second ILD layer, a patterned conductive layer served as a pixel electrode, a patterned third ILD layer, a plurality of contact windows in the first, second and third ILD layers for exposing the source, the drain, parts of the patterned conductive layer and the first electrode, a second electrode and a source/drain conductive line, the semiconductor structure with the multi-layer storage is obtained in consequence.