Semiconductor structures and fabrication methods thereof are provided. The method includes providing a substrate; forming a stacked material structure on the substrate; and forming trenches in the stacked material structure. Bottoms of the trenches are in the first material layer, the trenches are arranged along a first direction and form an initial stacked structure sequentially including an initial first layer, an initial second layer and an initial third layer. The method also includes etching the initial third layer to form transitional third layers arranged along a second direction perpendicular to the first direction; removing a portion of the initial first layer and a portion of the initial second layer of the initial stacked structure at two sides along the second direction to form a stacked structure including a first layer, a second layer and the transitional third layers; and forming a gate structure.