The invention provides a 3D storage device and manufacture method thereof. The 3D storage device includes a core zone and a step zone. The step zone includes a grid electrode isolating structure perpendicular to an extending face of the step zone; and a virtual channel structure adjacent to the grid electrode isolating structure and perpendicular to the extending face of the step zone, wherein oneof the upper surface of the grid electrode isolating structure and the upper surface of the virtual channel structure is taken as a reference plane while the other is not lower than the reference plane; the maximal feature dimension of the virtual channel structure is disposed at a first position of the virtual channel structure, the maximal feature dimension of the grid electrode isolating structure is disposed at a second position of the grid electrode isolating structure, and the first position and/or the second position are disposed below the reference plane. According to the invention, short circuit risks between the virtual channel structure and the grid electrode isolating structure is reduced.