A memory device and a manufacturing method thereof are provided. The memory device includes a gate stacking structure, a first insulating layer, a second insulating layer and a first spacer. The gate stacking structure is disposed over a substrate. The first insulating layer covers a top surface and a sidewall of the gate stacking structure. The second insulating layer covers a surface of the first insulating layer. A top corner region of the gate stacking structure is covered by the first and second insulating layers. The first spacer is located on the sidewall of the gate stacking structure, and covers a surface of the second insulating layer. A topmost end of the first spacer is lower than a topmost surface of the second insulating layer.