Crystal orientation is considered a pivotal factor influencing phase transformation of shape memory alloys (SMAs), which has been confirmed by comparing several specific orientations. A comprehensive atomic-scale understanding of the physical mechanisms of the crystal orientation effects could significantly contribute to the development of high-performance SMAs. This study systematically explores the dependence of the transformation behavior of NiTi SMA on the crystal orientation, focusing on preferred martensite variants and their corresponding energy evolutions, utilizing molecular dynamic simulations. The research reveals that crystal orientation plays a crucial role in selecting preferred martensite variants during phase transformation from austenite to martensite phase, and the selection rules can be predicted through a simple theoretical model based on the minimum free energy criterion. This phenomenon leads to a non-monotonic variation in the energy barriers during phase transformation and the mechanical properties, such as transformation stress and energy hysteresis, with the crystal orientation. Furthermore, the study validates the significance of this understanding in developing high-performance bicrystal SMA by constructing crystal grains with different orientations.