A method for forming bottle trenches. The method comprises providing a substrate formed with a pad stack layer on the top, and a deep trench with protective layer on the upper portions of sidewalls thereof, implanting ions into the lower portions of sidewalls and bottom of the trench not covered by the protective layer to amorphize the atomic structure of the sidewalls and bottom, oxidizing the amorphous sidewalls and bottom of the trench to form a bottle-shaped oxide layer thereon, and removing the bottle-shaped oxide layer.