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