A package structure and method of manufacturing a package structure are provided. The package structure comprises two semiconductor structures and two bonding layers sandwiched between both semiconductor structures. Each bonding layer has a plurality of bonding pads separated by an isolation layer. Each bonding pad has a bonding surface including a bonding region and at least one buffer region. The bonding regions in both bonding layers bond to each other. The buffer region of one semiconductor structure bonds to the isolation layer of the other semiconductor structure. A ratio of a surface area of the buffer region to that of the bonding region in each metal pad is from about 0.01 to about 10.