Femtosecond (fs) laser ablating CuZr amorphous alloy is investigated with molecular dynamics (MD) simulation combined with two temperature models. The duration of laser pulse is 200 fs and the fluence is regulated from 30 mJ/cm2 to 45 mJ/cm2. The results indicate that thermal diffusion of CuZr glass metal is much more slowly as compared with crystalline metal; tensile stresses is observed in target at first;the average size and the number of the gas bubbles generate inside the target are strongly dependent on the laser fluence; photomechanical effects are the main ablation mechanism,and ablation depth increases with fluence. It is helpful to understand the mechanism of interaction between femtosecond laser and amorphous alloy.