The present disclosure provides a method of manufacturing a semiconductor structure. The method includes: providing a substrate; forming a bit line structure over the substrate; forming a spacer surrounding the bit line structure; forming a polysilicon layer covering the bit line structure and the spacer; performing a first etching operation on the polysilicon layer to obtain a first height of the polysilicon layer, wherein the first height is less than a height of the bit line structure or a height of the spacer; performing a second etching operation on a first portion of the spacer; and performing a third etching operation on the polysilicon layer to obtain a second height of the polysilicon layer, wherein the second height is less than the first height.