A method of fabricating a semiconductor structure includes the following steps: forming a first interlayer dielectric on a substrate; forming a gate electrode on the substrate so that the periphery of the gate electrode is surrounded by the first interlayer dielectric; forming a patterned mask layer comprising at least a layer of organic material on the gate electrode; forming a conformal dielectric layer to conformally cover the layer of organic material; and forming a second interlayer dielectric to cover the conformal dielectric layer.