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 device layer is formed on a first substrate. A first bonding layer including a first bonding contact is formed above the first device layer. A first capping layer is formed at an upper end of the first bonding contact. The first capping layer has a conductive material different from a remainder of the first bonding contact. A second device layer is formed on a second substrate. A second bonding layer including a second bonding contact is formed above the second device layer. The first substrate and the second substrate are bonded in a face-to-face manner, so that the first bonding contact is in contact with the second bonding contact by the first capping layer.