The 0.532-\mum laser conditioning of HfO2/SiO2 third harmonic separator fabricated by electron-beam evaporation (EBE) was studied. The laser induced damage threshold (LIDT) of the separator determined by 1-on-1 test is 9.1 J/cm2 and it is 15.2 J/cm2 after laser conditioning determined by raster scanning. Two kinds of damage morphologies, taper pits and flat bottom pits, are found on the sample surface and they show different damage behaviors. The damage onset of taper pits does not change obviously and the laser conditioning effect is contributed to the flat bottom pits, which limits the application of laser conditioning.