The invention discloses a semiconductor structure and a manufacturing method thereof. The method comprises steps: a base is provided, wherein the base comprises a substrate and fin parts protruding against the substrate; a gate structure which crosses over the fin parts and covers the top surfaces and the side wall surfaces of part of the fin parts is formed; the fin parts at two sides of the gatestructure are removed, and grooves with the substrate exposed are formed at two sides of the gate structure; the substrate at the bottom part of the groove is internally provided with an anti-diffusion doping area; and after the anti-diffusion doping area is formed, a stress layer is formed in the groove, and a source-drain doping area is formed in the stress layer. After the grooves with the substrate exposed are formed at two sides of the gate structure, the substrate at the bottom part of the groove is internally provided with the anti-diffusion doping area; later, after the stress layer is formed in the groove and the source-drain doping area is formed in the stress layer, the anti-diffusion doping area is located in the substrate at the bottom part of the source-drain doping area, the anti-diffusion doping area can suppress diffusion of doping ions of the source-drain doping area to a channel area, bottom through can be prevented from happening to the source-drain doping area, and channel leakage current can thus be reduced.