A manufacturing method of a semiconductor device includes at least the following steps. A sacrificial substrate is provided. An epitaxial layer is formed on the sacrificial substrate. An etch stop layer is formed on the epitaxial layer. Carbon atoms are implanted into the etch stop layer. A capping layer and a device layer are formed on the etch stop layer. A handle substrate is bonded to the device layer. The sacrificial substrate, the epitaxial layer, and the etch stop layer having the carbon atoms are removed from the handle substrate.