The present invention provides a semiconductor structure and a manufacturing method thereof. The method includes providing a semiconductor substrate including a first region and a second region; and forming a first and a second metal-oxide-semiconductor (MOS) device. The step of forming the first MOS device includes forming a first silicon germanium layer over the first region of the semiconductor substrate; forming a silicon layer over the first silicon germanium layer; forming a first gate dielectric layer over the silicon layer; and patterning the first gate dielectric layer to form a first gate dielectric. The step of forming the second MOS device includes forming a second silicon germanium layer over the second region of the semiconductor substrate; forming a second gate dielectric layer over the second silicon germanium layer with no substantially pure silicon layer therebetween; and patterning the second gate dielectric layer to form a second gate dielectric. The invention can improve the drive current of NMOS element and reduce the leakage current of the PMOS element.