The invention provides a method for fabricating a memory device. At first, a substrate having a plurality of gate electrode stacks and a source/drain region is provided, and a barrier layer and a sacrificial layer are sequentially formed on the substrate and cover the gate electrode stacks. A portion of the sacrificial layer is removed to form a sacrificial plug between the gate electrode stacks, and then a filling layer is formed over the substrate. Next, the sacrificial plug is removed, and a contact hole is formed. A clean step with a solution containing ammonia is carried out. The barrier layer at the bottom of the contact hole is removed, and a metal plug is then formed in the contact hole to electrically contact with the source/drain region.