A method for fabricating a semiconductor device includes providing a base wafer comprising a scribing portion; bonding a first stacked die and a second stacked die onto a front surface of the base wafer through a hybrid bonding process; conformally forming a re-fill layer to cover the first stacked die and the second stacked die; forming a first molding layer to cover the re-fill layer and configure an intermediate semiconductor device comprising the base wafer, the first stacked die, the second stacked die, the re-fill layer, and the first molding layer; and dicing the intermediate semiconductor device along the scribing portion to separate the first stacked die and the second stacked die, the re-fill layer, the first molding layer, and the base wafer.