A semiconductor package structure includes a first semiconductor wafer including a first bonding pad. The semiconductor package structure also includes a second semiconductor wafer including a second bonding pad and a third bonding pad. The second bonding pad and the third bonding pad are bonded to the first bonding pad of the first semiconductor wafer. The semiconductor package structure further includes a first via penetrating through the second semiconductor wafer to physically contact the first bonding pad of the first semiconductor wafer. A portion of the first via is disposed between the second bonding pad and the third bonding pad.