The invention provides a manufacturing method of a semiconductor device. The method includes the following steps: a semiconductor substrate is provided and a through silicon via is formed in the semiconductor substrate; a first stress absorption layer and a copper conductive layer are sequentially formed in the through silicon via, wherein the top of the copper conductive layer at the bottom of the through silicon via is lower than the top of the through silicon via so as to partly fill the through silicon via; a second stress absorption layer is formed to cover the copper conductive layer and fill completely the through silicon via at the same time; and chemical mechanical polishing is executed until the top of the through silicon via is exposed. According to the method, the double stress absorption layers are formed in the through silicon via so that the internal stress at interfaces of a linear layer, a barrier layer and a copper conductive layer can be reduced significantly and happening of a stratification phenomenon can be prevented.