Embodiments of bonded semiconductor structures and fabrication methods thereof are disclosed. In an example, a method for forming a semiconductor device is disclosed. A first interconnect layer including first interconnects is formed above a first substrate. A first bonding layer including first bonding contacts is formed above the first interconnect layer, such that each first interconnect is in contact with a respective first bonding contact. A second interconnect layer including second interconnects is formed above a second substrate. A second bonding layer including second bonding contacts is formed above the second interconnect layer, such that at least one second bonding contact is in contact with a respective second interconnect, and at least another second bonding contact is separated from the second interconnects. The first and second substrates are bonded in a face-to-face manner, such that each first bonding contact is in contact with one second bonding contact at a bonding interface.