Embodiments of bonded semiconductor structures and fabrication methods thereof are disclosed. In an example, a semiconductor device includes a first semiconductor structure, a second semiconductor structure, and a bonding interface between the first and second semiconductor structures. The first semiconductor structure includes a substrate, a first device layer disposed on the substrate, and a first bonding layer disposed above the first device layer and including a first bonding contact. The second semiconductor structure includes a second device layer, and a second bonding layer disposed below the second device layer and including a second bonding contact. The first bonding contact is in contact with the second bonding contact at the bonding interface. At least one of the first bonding contact and the second bonding contact includes a capping layer at the bonding interface and having a conductive material different from a remainder of the respective first or second bonding contact.