A memory device and a manufacturing method thereof are provided. The memory device includes a first gate structure, a second gate structure, an oxide layer and a nitride layer. The first gate structure and the second gate structure are disposed on a substrate. The oxide layer covers the first gate structure. The nitride layer is disposed on the substrate and covers the oxide and the second gate structure. The refraction index of a portion of the nitride layer adjacent to an interface between the nitride layer and each of the first gate structure and the second gate structure is about 5% to 10% less than the refraction index of the remaining portion of the nitride layer.