A memory device and a manufacturing method thereof are provided. The memory device includes a word line, a bit line, an active region and a bit line contact structure. The word line is disposed in the substrate, and extends along a first direction. The bit line is disposed over the substrate, and extends along a second direction. The active region is disposed in the substrate, and extends along a third direction. The bit line contact structure is disposed between the active region and the bit line. A top view pattern of the bit line contact structure has a long axis. An angle between the extending direction of this long axis and the third direction is less than an angle between the extending direction of this long axis and the first direction, and is less than an angle between the extending direction of this long axis and the second direction.