In accordance with an embodiment, a manufacturing method of a semiconductor device includes: respectively forming a first layer and a second layer at the top of a protruding portion and at the bottom of a depressed portion of a treatment target having protrusions/depressions in such a manner that sidewalls of the protruding portion is exposed, supplying a treatment liquid to the treatment target having the first layer and the second layer, bringing a catalyst into contact with or closer to the first layer and thereby increasing the dissolution rate of the first layer in dissolving into the treatment liquid and dissolving the first layer into the treatment liquid, and sequentially dissolving the protruding portion and the second layer into the treatment liquid after the dissolution of the first layer.