Embodiments of through array contact structures of a 3D memory device and fabricating method thereof are disclosed. The 3D NAND memory device includes an alternating layer stack disposed on a substrate. The alternating layer stack includes a first region including an alternating dielectric stack, and a second region including an alternating conductor/dielectric stack. The memory device further comprises a barrier structure extending vertically through the alternating layer stack to laterally separate the first region from the second region, and multiple through array contacts in the first region each extending vertically through the alternating dielectric stack. At least one through array contact is electrically connected with a peripheral circuit.