Monocrystalline silicon-based microstructure functional surfaces are widely used in the field of photoelectricity. However, the traditional process is prone to damage due to the hardness and brittleness of monocrystalline silicon. In this study, the depth, width, and depth-width ratio of the micro-V-groove on the surface of monocrystalline silicon were studied using laser-assisted waterjet technology. Firstly, the nanosecond laser pulse width was optimized to minimize processing damage. Then, the response surface method (RSM) was employed to optimize the V-groove’s depth-width ratio and show the process parameters’ interactive effects. The results show that the heated affected zone (HAZ) and lattice disorder at 10 ns are significantly smaller than those at other pulse widths, and there is almost no amorphous phase on the surface of V-grooves. Single process parameter usually has different effects on the size of the V-groove, and the process parameters have significant interactive effects, which are discussed in detail in the study. According to the prediction model, the highest depth-width ratio of a V-groove is 1.39. Near-damage-free V-groove with a high depth-width ratio helps to lower the reflectivity and increase the hydrophobicity of monocrystalline silicon.