Due to the unique properties of femtosecond laser in precision machining, femtosecond laser was utilized for irradiation on SiC/SiC composites. Effects of different processing parameters, including the spot overlap ratio, helical line overlap ratio, laser processing power, as well as processing steps, were discussed in detail. The results indicated that the parameters above had significant effect on machining of SiC/SiC composites. The surface morphology and geometry of the micro-holes were investigated under different parameters, and the corresponding formation mechanism was discussed in detail. It was believed that both the spot and helical line overlap ratio had great effect on the quality of the micro-holes and would be responsible to the depth of micro-holes. Besides, it is indicated that the higher processing power will lead to a better quality of surface morphology and machining results. In micro-hole drilling process, debris and fragments were observed within the micro-holes, and XPS analysis showed that there existed Si-O bonds and Si-C bonds, indicating that the oxidation during processing was incomplete. In addition, the effect of feeding speeds on geometry and depth of the micro-holes were discussed as well.