As semiconductor devices become extremely integrated and their geometry continues to shrink, even slight critical dimension (CD) move or phase decay during photomask cleaning may have a negative impact on the CD uniformity performance of photomask. In addition, the printing of sub-resolution assist-features (SRAF) on photomask becomes the main limiting factor in using high power and low frequency Mega-sonic cleaning process, therefore, the balance between SRAF damage and clean performance becomes extremely important. In this research, the CD movement both on Chrome layer and MoSi layer and the phase and transmission decay on MoSi layer of advanced PSM photomask induced by Tetra-Methyl-Ammonium-Hydroxide (TMAH) based cleaning process were studied. Meanwhile, the difference between TMAH and SC1 were emphasized. The results showed that TMAH has significant advantage in CD move and phase decay. We also researched the SRAF damage condition after cleaning by the chemical of TMAH with Multi-Beam and Multi-Frequency (MBMF) mode. In addition, we collected different kinds of particles to study the particle remove capability of TMAH under MBMF mode.