In order to study the effect of different crystal orientation on femtosecond laser processing of silicon. A 515 nm green high power femtosecond laser was used to ablate Si(111) and Si(100) by changing the average laser power and scanning times. The difference of groove ablation depth and groove bottom roughness between the two crystal planes was compared. Electron backscatter diffraction (EBSD) was used to study the micro behavior of different crystal faces in femtosecond laser ablation. The amorphization threshold and ablation threshold of different crystal faces were compared, and meanwhile the amorphization ability and recrystallization ability of different crystal faces were compared. With the increase of average laser power and scanning times, the groove formed by laser ablation becomes deeper and deeper. Under the same conditions, the groove depth of Si(111) is greater than that of Si(100), and the groove bottom roughness of Si(111) is greater than that of Si(100). When the groove depth reaches 300 μm, the groove depth of Si(111) is about 20 μm deeper than that of Si(100), the roughness of Si(111) is about 4 μm high than that of Si(100). The amorphous thresholds of the two silicon planes were obtained by EBSD technique, which were approximately 0.16 J/cm2. At the same amorphization threshold, the degree of amorphization of Si(111) is greater than that of Si(100). It is observed that the laser absorptivity of Si(111) is higher than that of the Si(100) with less laser scanning times. The crystal orientation not only affects the microstructure of silicon under the action of femtosecond laser multi pulse, but also affects the effect of femtosecond laser processing. When the processing parameters are the same, the ablation depth of Si(111) is significantly greater than that of Si(100), because the amorphous ability of Si(111) is stronger than that of Si(100), which leads to more laser energy absorption and higher material removal efficiency of Si(111).