Embodiments of through array contact structures of a 3D memory device and fabricating method thereof are disclosed. The method comprises: forming a recess region in a substrate including multiple protruding islands; forming a gate dielectric layer to cover top surfaces and sidewalls of the multiple protruding islands and a top surface of the recess region of the substrate; forming an underlying sacrificial layer on the gate dielectric layer to surround the sidewalls of the multiple protruding islands; forming an alternating dielectric stack including multiple alternatively stacked insulating layers and sacrificial layers on the underlying sacrificial layer and the multiple protruding islands; forming multiple channel holes penetrating the alternating dielectric stack, each channel hole is located corresponding to one of the multiple protruding islands; and forming a memory layer in each channel hole, wherein a channel layer of the memory layer is electrically connected with a corresponding protruding island.