A semiconductor structure and a forming method thereof are disclosed. The semiconductor structure comprises a substrate including a first area and a second area which are adjacent to each other, and of which the surfaces are provided fin portions respectively, an isolation groove positioned in the substrate and between the first area and the second area, and an isolating layer which is positioned on the surface of the substrate in the isolation groove, fills the isolation groove, and also is positioned on partial surface of the fin portions. The surface of the isolating layer is lower than the top surfaces of the fin portion. The semiconductor structure also comprises first well regions in the substrate of the first area and the fin portions, and a second well regions in the substrate of the second area and the fin portions. The performance of the semiconductor structure is improved.