A method of manufacturing a semiconductor device includes alternately stacking sacrificial layers and interlayer insulating layers on a substrate, to form a stack structure; forming channels penetrating through the stack structure; forming separation regions penetrating through the stack structure; forming lateral openings by removing the sacrificial layers through the separation regions; and forming gate electrodes in the lateral openings. Forming the gate electrodes may include forming a nucleation layer in the lateral openings by supplying a source gas and a first reaction gas, and forming a bulk layer on the nucleation layer to fill the lateral openings by supplying the source gas and a second reaction gas, different from the first reaction gas. The first reaction gas may be supplied from a first reaction gas source, stored in a gas charging unit, and supplied from the gas charging unit.