The invention provides a semiconductor structure and a manufacturing method thereof. The manufacturing method of the semiconductor structure includes the following steps. A first isolation layer is formed on a first surface of a wafer substrate. A conductive pad is formed on the first isolation layer. A hollow region through the first surface and a second surface of the wafer substrate is formed, such that the first isolation layer is exposed through the hollow region. A laser etching treatment is performed on the first isolation layer that is exposed through the hollow region, such that a first opening is formed in the first isolation layer, and a concave portion exposed through the first opening is formed in the conductive pad. According to the invention, the yield rate of the semiconductor structure may be improved. Moreover, the thickness of the conductive pad may be decreased for saving cost.