A method of fabricating self-aligned gate trench utilizing TTO poly spacer is disclosed. A semiconductor substrate having thereon a pad oxide layer and pad nitride layer is provided. A plurality of trench capacitors are embedded in a memory array region of the semiconductor substrate. Each of the trench capacitors has a trench top oxide (TTO) that extrudes from a main surface of the semiconductor substrate. Poly spacers are formed on two opposite sides of the extruding TTO and are used, after oxidized, as an etching hard mask for etching a recessed gate trench in close proximity to the trench capacitor.