The invention relates to a method of forming an epitaxial structure in channel holes of a three dimensional memory device. The method includes the steps: providing a semiconductor structure which includes a core area and an auxiliary area, wherein the core area has channel holes and the auxiliary area has dummy holes and/or trenches; forming a first epitaxial structure at the bottom of the channelholes, and forming a second epitaxial structure at the bottom of the dummy holes and/or trenches; and using a photoetching step for the auxiliary area to remove the second epitaxial structure at thebottom of the dummy holes and/or trenches. The method of forming an epitaxial structure in channel holes of a three dimensional memory device can solve the electric leakage and reliability risk causedby the epitaxial structures and can simplify the process difficulty at the same time as the epitaxial structure is formed in the channel holes of the core area and no epitaxial structure is formed inthe dummy holes and/or trenches of the auxiliary area.