According to an exemplary embodiment, a method of forming a semiconductor device is provided. The method includes: providing a vertical structure over a substrate; forming an etch stop layer over the vertical structure; forming an oxide layer over the etch stop layer; performing chemical mechanical polishing on the oxide layer and stopping on the etch stop layer; etching back the oxide layer and the etch stop layer to expose a sidewall of the vertical structure and to form an isolation layer; oxidizing the sidewall of the vertical structure and doping oxygen into the isolation layer by using a cluster oxygen doping treatment.