Diameters of morphology zones of crater processed by femtosecond laser were measured in the range of laser fluence from 0.108J/cm2 to 28.68J/cm2. Thermal melting on the surface of a hole and the heat conduction rule were studied. The melting zones were calculated according to the traditional thermal conduction formula. The calculated results matched with the experiment results very well. It suggested that the thermal diffusion in super power femtosecond laser micromachining was inevitable. Besides, reasonable parameters were acquired for the better quality of the micro-holes.