A 3D memory device, including: a first memory layer including a first memory transistor with side gates; a second memory layer including a second memory transistor with side gates; and a periphery circuits layer including logic transistors for controlling the memory, the periphery circuits are covered by a first isolation layer, where the first memory layer includes a first monolithically mono-crystal layer directly bonded to a second isolation layer, and the second memory layer includes a second monolithically mono-crystal layer directly bonded to the second isolation layer, and the first mono-crystal layer is bonded on top of the first isolation layer, and the second memory transistor is self-aligned to the first memory transistor.