Embodiments of three-dimensional (3D) memory devices formed by bonded semiconductor devices and methods for forming the same are disclosed. In an example, a method for forming a bonded semiconductor device includes the following operations. First, a first wafer and a second wafer are formed. The first wafer can include a functional layer over a substrate. Single-crystalline silicon may not be essential to the substrate and the substrate may not include single-crystalline silicon. The first wafer can be flipped to bond onto the second wafer to form the bonded semiconductor device so the substrate is on top of the functional layer. At least a portion of the substrate can be removed to form a top surface of the bonded semiconductor device. Further, bonding pads can be formed over the top surface.