The present invention provides a method for manufacturing contact holes in a CMOS device by using a gate-last process, comprising: forming high-K dielectrics/metal gates (HKMG) of a first type MOS; forming and metalizing lower contact holes of the source/drain of a first type MOS and a second type MOS as well as forming HKMG of a second type MOS simultaneously, wherein the lower contact holes of the source/drain are filled with the same material as that used by the metal gate of the second type MOS; forming and metalizing contact holes of metal gates of a first type MOS and a second type MOS as well as upper contact holes of the source/drain, wherein the upper contact holes of the source/drain are aligned with the lower contact holes of the source/drain. The method reduces the difficulty of contact hole etching and metal deposition, simplifies the process steps, and increases the reliability of the device.