A semiconductor device is provided. The semiconductor device includes a semiconductor substrate including a first doped region and a second doped region and a gate stack on the semiconductor substrate. The semiconductor device also includes a main spacer layer on a sidewall of the gate stack and a protection layer between the main spacer layer and the semiconductor substrate. The protection layer is doped with a quadrivalent element. The semiconductor device further includes an insulating layer formed over the semiconductor substrate and the gate stack and a contact formed in the insulating layer. The contact includes a first portion contacting the first doped region, and the contact includes a second portion contacting the second doped region. The first portion extends deeper into the semiconductor substrate than the second portion.