The formation mechanism of Laser Induced Periodic Surface Structures (LIPSS) on the amorphous alloy Zr44Ti11Cu10Ni10Be25(at%) was investigated. In experiment, LIPSS on the amorphous alloy were produced by ultrashort laser pulses of 120 fs duration at 800 nm wavelength in three types of laser polarizations (linear, radial and azimuthal polarization). These LIPSS are comprised of Low-Spatial-Frequency LIPSS (LSFL) with the periodicity of 652～723 nm and macro-ripples with the periodicity of 1 304～1 765 nm. By Finite-Difference Time-Domain (FDTD) simulations, formation mechanism of macro-ripples can be explained by the interference between laser and modulated scattered electromagnetic wave induced by rough surface. In the condition of three types of laser polarizations (linear, radial and azimuthal polarization), FDTD simulation results agree with experimental results, proving the effectiveness of the macro-ripple formation mechanism.