Semiconductor structures and fabrication methods thereof are provided. An exemplary fabrication method includes providing a semiconductor substrate having a first region, a second region and an isolation region between the first region and the second region; forming a plurality of first fins on the semiconductor substrate in the first region and a plurality of second fins on the semiconductor substrate in the second region; forming an isolation structure, covering portions of side surfaces of the first fins and the second fins and with a top surface below the top surfaces of the first fins and the second fins, over the semiconductor substrate; and forming an isolation layer over the isolation structure in the isolation region and with a top surface coplanar or above the top surfaces of the first fins and the second fins.