A manufacturing method of a semiconductor device includes forming a contact opening in a wafer. The wafer includes a substrate, a gate structure over the substrate and a dielectric layer over the substrate and surrounding the gate structure, and the contact opening passes through the dielectric layer and exposes the substrate. A recess is formed in the substrate such that the recess is connected to the contact opening. An oxidation process is performed to convert a portion of the substrate exposed in the recess to form a protection layer lining a sidewall and a bottom surface of the recess. The protection layer is etched back to remove a first portion of the protection layer in contact with the bottom surface of the recess of the substrate. A metal alloy structure is formed at the bottom surface of the recess of the substrate.