In a manufacturing method of a semiconductor structure, a substrate having a front surface and a back surface is provided. The front surface has a device layer thereon and conductive plugs electrically connected to the device layer. A thinning process is performed on the back surface of the substrate, such that the back surface of the substrate and surfaces of the conductive plugs have a distance therebetween. Holes are formed in the substrate from the back surface to the conductive plugs, so as to form a porous film. An oxidization process is performed, such that the porous film correspondingly is reacted to form an oxide material layer. A polishing process is performed on the oxide material layer to expose the surfaces of the conductive plugs.