A method of fabricating a semiconductor device includes: forming a first transistor including: forming a plurality of lightly doped regions in a substrate; forming a first gate structure on the substrate, the first gate structure covering portions of the plurality of lightly doped regions and a portion of the substrate; forming first spacers on sidewalls of the first gate structure; forming doped region in the lightly doped regions; forming an etching stop layer on the substrate; patterning the etching stop layer and the first gate structure to form a second gate structure, and to form a plurality of trenches between the second gate structure and the first spacers; and forming a first dielectric layer on the substrate to cover the etching stop layer and fill the plurality of trenches. The first dielectric layer filled in the trenches is used as virtual spacers.