The morphologies of silicon surfaces are modified with the single Nd:YAG nanosecond laser pulse (wavelength 532 nm) in the air and water. The influence of laser induced plasma shock waves in the medium/silicon interface on silicon surface topography is studied. The shock wave mechanical signals are gathered by piezoelectric sensors and the morphology of silicon surfaces is observed by scanning electron microscopes (SEM). It is found that at the same energy level, the average speed of the underwater shock wave generated by irradiating the silicon surface under water is 1.5~2 times higher than that in air, and the mechanical strength under water is about 10 times higher than that in air. By observing the silicon surface morphology, it is found that many raised bulbs and recessed holes appears at the center of the craters on silicon surface under water, with corrugated structure but no sediment at the edges. While the center of the craters on silicon surface in air are relatively smooth, with circles of sediment at the edges. Thermal-mechanical effect induced by plasma shock waves generated at the medium/silicon interface is the main reason of silicon surface topography formation. Under water, greater mechanical strength of the shock wave induced by restriction effect of water, and explosive boiling thermal phenomena result in completely different topography as compared with those in air.