Surface effect on phase transformation of single crystal (SC) NiTi shape memory alloys (SMAs) with various thicknesses and various Ni contents is studied by molecular dynamics simulation. For the SMAs with various thicknesses considering surface effect, the residual strain, the average atomic potential energy, and the four characteristic phase transformation temperatures all increase, and fewer twinned martensite boundaries are left after cooling compared to the sample without considering surface effect. Moreover, with increasing thickness of the sample, the surface effect is gradually weakened, and there is no obvious regularity in phase transformation characteristics. For the SMAs with various Ni contents considering surface effect, segmental martensite phase transformation, phase transformation fluctuation, and wider phase transformation temperature ranges are observed, whereas these phenomena do not occur in the sample without considering surface effect. With the increasing of Ni contents, for both cases of considering surface effect or not, the critical stress of phase transformation, average atomic potential energy, the modulus of detwinned martensite increase, but the phase transformation temperature and modulus of twinned martensite decrease.