Embodiments of three-dimensional (3D) memory devices have a hydrogen blocking layer and fabrication methods thereof are disclosed. In an example, a method for form a 3D memory device is disclosed. An array of NAND memory strings each extending vertically above a first substrate are formed. A plurality of logic process-compatible devices are formed on a second substrate. The first substrate and the second substrate are bonded in a face-to-face manner. The logic process-compatible devices are above the array of NAND memory strings after the bonding. The second substrate is thinned to form a semiconductor layer above and in contact with the logic process-compatible devices.