Porosity can change the phase transformation behaviors of the NiTi Shape Memory Alloys (SMAs). In this work, the dependence of porosity of nanocrystalline (NC) NiTi SMAs on martensite transformation deformation mechanism is studied by molecular dynamics (MD) simulation. The effects of porosity on martensite transformation deformation mechanism of NC NiTi SMAs are studied under an isothermal condition. The simulation results show that the threshold temperatures of phase transformation and residual strain of NC NiTi SMAs increase with the increasing porosity, while the threshold stresses of phase transformation of NC NiTi SMAs decrease with the increasing porosity. Furthermore, the effects of loading types, peak stresses and initial temperatures on martensite transformation deformation mechanisms of NC porous NiTi SMAs are analyzed. The results show that the threshold stresses of phase transformation of NC porous NiTi SMAs increases with the increase of temperature and peak stress, and residual strain increases with the decrease of temperature or the increases of peak stress. These results are helpful to further understand the phase transformation behavior of NC porous NiTi SMAs at the atomic scale.