The ablation mechanism of the femtosecond laser ablating B2 type NiTi alloy is studied by the molecular dynamics simulation combined with two-temperature model. The target material thickness of 90 nm is ablated by the laser with the central wavelength of 800 nm, energy density of 29.3 mJ/cm2 and pulse durations of 50, 200, 500 and 1000 fs. The pressure-transmitting boundary condition for the bottom of the target material is formulated, the result shows that the condition is adapted to the simulation. The temperature and internal pressure with time varying and atomic configuration in the target material show the influences of pulse durations on ablation process. The result shows that the peak temperature of electron in center irradiation zone is lower, the pulse duration is wider at the same energy density, but the peak temperature of lattice in center irradiation zone is higher, the heat affect zone is greater. The ablation is occurred when the pulse durations are 200, 500 and 1 000 fs.