A pad structure adapted to be disposed on a first package substrate and electrically connected to conductive contacts of a second package substrate includes a first conductive pad having a first top surface, a second conductive pad, a first leveling conductor and a second leveling conductor. The second conductive pad disposed aside the first conductive pad has a second top surface non-coplanar with the first top surface. The first leveling conductor disposed on the first conductive pad has a first leveling surface opposite to the first top surface. The second leveling conductor disposed on the second conductive pad and having a second leveling surface opposite to the second top surface is coplanar with the first leveling surface. The conductive contacts of the second package substrate are disposed on the first leveling conductor and the second leveling conductor. A manufacturing method of a pad structure is also provided.