Semiconductor structures and fabrication methods thereof are provided. An exemplary fabrication method includes providing a base substrate; forming a dummy gate structure over the base substrate; forming source/drain regions having source/drain doping ions in the base substrate at both sides of the dummy gate structure; forming a dielectric layer on the source/drain regions and covering the side surfaces of the dummy gate structure; removing the dummy gate structure to form an opening in the dielectric layer; performing one or more of a first ion implantation process, for implanting first barrier ions in the base substrate toward the source region to form a first barrier layer under the opening, and a second ion implantation process, for implanting second barrier ions in the base substrate toward the source region to form a second barrier layer under the opening; and forming a gate structure in the opening.