A manufacturing method of an epitaxial fin-shaped structure includes the following steps. A substrate is provided. A recess is formed in the substrate. An epitaxial layer is formed on the substrate. The epitaxial layer is partly formed in the recess and partly formed outside the recess. The epitaxial layer has a dent formed on the top surface of the epitaxial layer, and the dent is formed corresponding to the recess in a thickness direction of the substrate. A nitride layer is conformally formed on the epitaxial layer. An oxide layer is formed on the nitride layer. A first planarization process is performed to remove a part of the oxide layer, and the first planarization process is stopped on the nitride layer. The epitaxial layer in the recess is patterned for forming at least one epitaxial fin-shaped structure.