A method for fabricating MEMS device includes providing a substrate having a first side and a second side. Then, a structural dielectric layer is formed over the substrate at the first side, wherein a structural conductive layer is embedded in the structural dielectric layer. A multi-stage patterning process is performed on the substrate from the second side, wherein a plurality of regions of the substrate with different levels is formed and a portion of the structural dielectric layer is exposed. An isotropic etching process is performed from the second side of the substrate or from the both side of the substrate to etch the structural dielectric layer, wherein a remaining portion of the structural dielectric layer comprises the structural conductive layer and a dielectric portion enclosed by the structural conductive layer.