Embodiments of mechanisms for forming a semiconductor device are provided. The semiconductor device includes a semiconductor substrate having a first doped region and a second doped region, and a gate stack formed on the semiconductor substrate. The semiconductor device also includes a main spacer layer formed on a sidewall of the gate stack. The semiconductor device further includes a protection layer formed between the main spacer layer and the semiconductor substrate, and the protection layer is doped with a quadrivalent element. In addition, the semiconductor device includes an insulating layer formed on the semiconductor substrate and the gate stack, and a contact formed in the insulating layer. The contact has a first portion contacting the first doped region and has a second portion contacting the second doped region. The first region extends deeper into the semiconductor substrate than the second portion.