Method is to fabricate a MEMS device with a substrate. The substrate has through holes in the substrate within a diaphragm region and optionally an indent space from the second surface at the diaphragm region. A first dielectric structural layer is then disposed over the substrate from the first surface, wherein the first dielectric structural layer has a plurality of openings corresponding to the through holes, wherein each of the through holes remains exposed by the first dielectric structural layer. A second dielectric structural layer with a chamber is disposed over the first dielectric structural layer, wherein the chamber exposes the openings of the first dielectric structural layer and the through holes of the substrate to connect to the indent space. A MEMS diaphragm is embedded in the second dielectric structural layer above the chamber, wherein an air gap is formed between the substrate and the MEMS diaphragm.