We experimentally investigate the differences in the evolution of surface-microstructured silicon fabricated by femtosecond laser pulses with different wavelength as a function of irradiated laser energy. The results show that when laser energy absorbed by the silicon material is the same, laser pulses with a shorter wavelength can form the surface-microstructured silicon with less laser energy, while the corresponding spike height is much lower than that of laser pulses with a longer wavelength. This is because the penetration depth of the laser pulses increases exponentially at the increase of the laser wavelength. Additionally, for two laser pulses with the certain wavelength and the certain absorption efficiency of silicon, the proportional relations between their formed spike height and irradiated laser energy should be determined. In particular, the average spike height is 3 times with 8 times corresponding energy for 800 nm laser pulses than that of 400 nm. These results are a benefit for the fast and optimum-morphology preparation of microstructured silicon.