A semiconductor structure and fabrication method thereof are provided. The fabrication method includes: providing a base substrate including a substrate and a plurality of fins on the substrate; forming gate structures across the fins, to cover a portion of sidewalls of the fins and a portion of top surfaces of the fins; forming stress layers in the fins on sides of each gate structure; forming barrier layers on sidewalls of the gate structure; and forming doped regions by applying first ion implantation processes to the fins under the stress layers using the barrier layers as a mask.