A method for forming isolation structure for MOS transistor is disclosed, which includes forming a first photoresist layer over a sacrificed oxide layer of a semiconductor substrate, patterning the first photoresist layer to define a PMOS active region and a PMOS isolation region; implanting nitrogen ions into the PMOS isolation region through the sacrificed oxide layer by using the first photoresist layer as a mask; removing the first photoresist layer; forming a second photoresist layer over the sacrificed oxide layer, patterning the second photoresist layer to define a NMOS active region and a NMOS isolation region; implanting oxygen ions into the NMOS isolation region through the sacrificed oxide layer by using the second photoresist layer as a mask; removing the second photoresist layer and the sacrificed oxide layer; and annealing the semiconductor substrate to form isolation structures of PMOS and NMOS, respectively.