A phase shifting mask repair process is described. The process uses an etching gas or a hydrofluoric acid solution to etch the quartz substrate and the characteristics of the phase shifter layer being only slightly etched when clean with a NH3/H2O2/H2O2 solution to calculate and adjust the respective processing time accordingly. As a result, the phase difference between the quartz substrate and the MoSiON phase shifter layer stays relatively the same before and after the repair process.