A vertical transistor structure comprises a substrate, a plurality of pillars formed on the substrate and spaced from each other, a plurality of trenches each formed between two adjacent pillars, a protection layer formed on the surface of a first side wall and the surface of a second side wall of the trench, a first gate and a second gate respectively formed on the protection layer of the first side wall and the second side wall, and a separation layer covering a bottom wall of the trench. The present invention uses the separation layer functioning as an etch stopping layer to the first gate and the second gate while being etched. Further, thickness of the separation layer is used to control the distance between the bottom wall and the first and second gates and define widths of the drain and the source formed in the pillar via ion implantation.