The invention discloses a semiconductor element and a manufacturing method thereof. The semiconductor element comprises a semiconductor substrate, a grid structure, at least one epitaxial layer, an interlayer dielectric layer, at least one contact hole, at least one metal silicide and a fluorine-containing layer. The semiconductor substrate is provided with at least one grid region and at least one source/drain region adjacent to the grid region. The grid structure is arranged in the grid region on the semiconductor substrate. The epitaxial layer is arranged in the source/drain region of the semiconductor substrate. The semiconductor substrate, the grid structure and the epitaxial layer are covered with the interlayer dielectric layer. The contact hole penetrates through the interlayer dielectric layer until the epitaxial layer is exposed outside . The metal silicide is located on the part, at the bottom of the contact hole, of the epitaxial layer. The fluorine-containing layer is arranged in or on the epitaxial layer and arranged on the periphery of a metal silicide layer.