A method of manufacturing a metal-oxide-semiconductor (MOS) transistor device is disclosed. A gate dielectric layer is formed on an active area of a substrate. A gate electrode is patterned on the gate dielectric layer. The gate electrode has vertical sidewalls and a top surface. A liner is formed on the vertical sidewalls of the gate electrode. A nitride spacer is formed on the liner. An ion implanted is performed to form a source/drain region. After salicide process, an STI region that isolates the active area is recessed, thereby forming a step height at interface between the active area and the STI region. The nitride spacer is removed. A nitride cap layer that borders the liner is deposited. The nitride cap layer has a specific stress status.