Embodiments of bonded semiconductor structures and fabrication methods thereof are disclosed. In an example, a semiconductor device includes a first and a second semiconductor structures. The first semiconductor structure includes a first interconnect layer including first interconnects. The first semiconductor structure further includes a first bonding layer including first bonding contacts. Each first interconnect is in contact with a respective first bonding contact. The second semiconductor structure includes a second interconnect layer including second interconnects. The second semiconductor structure further includes a second bonding layer including second bonding contacts. At least one second bonding contact is in contact with a respective second interconnect. At least another second bonding contact is separated from the second interconnects. The semiconductor device further includes a bonding interface between the first and second bonding layers. Each first bonding contact is in contact with one of the second bonding contacts at the bonding interface.