A method of manufacturing a semiconductor device having a combination structure of a horizontal oxide layer structure and a vertical oxide layer structure, can include: etching from an upper surface of the semiconductor substrate to inside of the semiconductor substrate to form a trench; depositing oxides in the trench to form the vertical oxide layer structure; etching the vertical oxide layer structure from an upper surface thereof to decrease height of the vertical oxide layer structure, and to make a top surface of the vertical oxide layer structure be below the upper surface of the semiconductor substrate, in order to expose side surfaces of the trench; and forming, by an oxidation process, the horizontal oxide layer structure to cover part of the upper surface of the semiconductor substrate and the upper surface of the vertical oxide layer structure.