A semiconductor device and a manufacturing method thereof are provided. In one embodiment of the manufacturing method of the semiconductor device, a through electrode is formed on a semiconductor die, and a dielectric layer such as a photopolymer is coated on the through electrode to cover the through electrode. Under exposure is performed on the dielectric layer, thereby partially removing the dielectric layer by development. As a result, a top end of the through electrode is exposed to the outside or protrudes through the dielectric layer. The dielectric layer remaining on the top end of the through electrode may be removed by performing a plasma descum process, if needed.