A forming method of an epitaxial layer, a forming method of a 3D NAND memory and an annealing apparatus are provided. In the forming method of the epitaxial layer, a first annealing process is performed for eliminating a stress generated in a stacked structure. When performing the first annealing process, a silicon-containing mixture is formed on a sidewall and a bottom surface of a trench. Thus, after performing the first annealing process, a second annealing process is performed for removing the silicon-containing mixture disposed at the sidewall and the bottom surface of the trench, such that when subsequently forming the epitaxial layer, a growth interface of the epitaxial layer is a pure substrate material interface, so as to prevent from be formed a void defect in the epitaxial layer formed in the trench.