Semiconductor packages and manufacturing methods thereof are provided. One of the semiconductor packages includes a first chip, a second chip and a molding compound. The first chip has at least one first via and a protection layer thereon, and the at least one first via is formed in the protection layer. The second chip has at least one second via thereon. The molding layer encapsulates the first and second chips. The at least one second via is disposed in and contact with the molding layer, and top surfaces of the protection layer, the at least one first via and the at least one second via are substantially coplanar with a top surface of the molding layer.