The mechanisms of femtosecond (fs) laser ablating nickel (Ni) and aluminum (Al) are investigated by molecular dynamics simulations combined with two-temperature model.The central wavelength of 800 nm,pulse durations of 70 fs or 200 fs and energy fluence from 0.043 J·cm－2 to 0.40 J·cm－2 are considered in the simulation respectively.The evolutions of temperature,atomic configuration and pressure distribution in the target materials reveal the influences of thermophysical parameters and laser parameters on ablation process.The results show that the electronic thermo-conductivity still has great influence on laser-metals interaction under femtosecond time-scale.Comparing the results of fs laser ablating Ni and Al,the nonequilibrium between the electron and lattice temperature of Al continued for a longer time as the electron-lattice coupling constant of Al is much smaller than that of Ni.The balance time for surface and bottom electronic temperature of Al became shorter as the electronic thermal conductivity of Al is much larger than that of Ni.Nanocrystal structures appeare on the surface of Al film ablated with laser fluence of 0.4 J·cm－2.