Stillinger–Weber potential and Z-layer energy model were adopted in molecular dynamics simulation to study the ablation of silicon by water-jet-guided femtosecond laser, and comparison was made by ablating silicon with or without water-jet cooling in our simulations. Simulation results indicated that with water-jet cooling, the thermal-affected zone could be reduced in area, and the peak of density could disappear more quickly. It was therefore concluded that water-jet-guided laser could be used to considerably improve the ablation quality of silicon.