A manufacturing method of a semiconductor structure for improving quality of an epitaxial layer is provided in the present invention. The manufacturing method includes the following steps. A gate structure is formed on a semiconductor substrate, and two lightly doped regions are formed in the semiconductor substrate at two sides of the gate structure. A capping layer is formed on the gate structure and the lightly doped regions. Two epitaxial layers are formed at the two sides of the gate structure after the step of forming the capping layer. An oxide film formed on the lightly doped regions will influence the growth condition of the epitaxial layers. A removing process is performed to remove the oxide film on the lightly doped regions before the step of forming the capping layer so as to improve the quality of the epitaxial layers.