A manufacturing method of a semiconductor structure includes the following steps. A patterned mask layer is formed on a semiconductor substrate. An isolation trench is formed in the semiconductor substrate by removing a part of the semiconductor substrate. A liner layer is conformally formed on an inner sidewall of the isolation trench. An implantation process is performed to the liner layer. The implantation process includes a noble gas implantation process. An isolation structure is at least partially formed in the isolation trench after the implantation process. An etching process is performed to remove the patterned mask layer after forming the isolation structure and expose a top surface of the semiconductor substrate. A part of the liner layer formed on the inner sidewall of the isolation trench is removed by the etching process. The implantation process is configured to modify the etch rate of the liner layer in the etching process.