A method for manufacturing a MOS transistor includes performing a thermal treatment to repair damaged substrate before forming source/drain extension regions, accordingly negative bias temperature instability (NBTI) is reduced. Since the thermal treatment is performed before forming the source/drain extension regions, heat budget for forming the source/drain extension regions and junction depth and junction profile of the source/drain extension would not be affected. Therefore the provided method for manufacturing a MOS transistor is capable of reducing short channel effect and possesses a superior process compatibility.