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 a fin part protruding against the substrate, the substrate comprises a first area and a second area, and the first area and the second area are used for forming different types of transistors; a gate dielectric layer covering the top part and the side wall of the fin part is formed; a blocking layer is formed on the gate dielectric layer at the junction of the first area and the second area, wherein the blocking layer at least covers the gate dielectric layer in the second area at the junction; a second work function layer is formed on the gate dielectric layer in the second area and the blocking layer; and a first work function layer is formed on the gate dielectric layer in the first area. The blocking layer is firstly formed on the gate dielectric layer at the junction of the first area and the second area, the blocking layer at least covers the gate dielectric layer in the second area at the junction, the blocking layer can reduce the diffusion degree of metal ions of the first work function layer in the second work function layer, and bad influences on the performance of the second work function layer can also be avoided.