Embodiments of bonded semiconductor structures and fabrication methods thereof are disclosed. In an example, a bonded structure includes a first bonding layer including a first bonding contact and a first bonding alignment mark, a second bonding layer including a second bonding contact and a second bonding alignment mark, and a bonding interface between the first bonding layer and the second bonding layer. The first bonding alignment mark is aligned with the second bonding alignment mark at the bonding interface, such that the first bonding contact is aligned with the second bonding contact at the bonding interface. The first bonding alignment mark includes a plurality of first repetitive patterns. The second bonding alignment mark includes a plurality of second repetitive patterns different from the plurality of first repetitive patterns.