A semiconductor structure and a manufacturing method thereof are provided. The semiconductor structure includes a substrate, a device layer and a least one conductive post. The substrate includes a first surface, a second surface opposite to the first surface, and at least one through hole penetrating the substrate. The substrate includes a first side wall portion and a second side wall portion at the through hole. The first side wall portion is connected to the first surface and includes a plurality of first scallops. The second side wall portion is connected to the second surface and includes a non-scalloped surface. The device layer is disposed on the second surface, and the second side wall portion of the substrate further extends into the device layer along the non-scalloped surface. The conductive post is disposed in the through hole, wherein the conductive post is electrically connected to the device layer.