Femtosecond laser has been widely utilized for modification of crystal structure to achieve desired functions. However, the effect of crystallographic orientation on the induced structure by femtosecond laser processing has yet been comprehensively studied. In this work, the crystallographic orientation dependence of amorphization effect of Si with femtosecond laser irradiation is studied. It is revealed that surfaces of different crystallographic orientations have different tendencies to form amorphization. Within the laser fluence range in this work, the (111) surface of Si favors generation of amorphization compared with the other crystallographic planes. This phenomenon could be explained by the lowest crystallization speed required by the (111) surface due to its smallest surface energy. Compared with nanosecond laser, non-thermal melting induced by femtosecond laser induces mild thermal gradient and favors recrystallization in the lattice.