Understanding phase transformation behaviors is essential for the material design of shape memory alloys (SMAs). This paper studies stress-induced phase transformation in single-crystal NiTi SMAs with three orientations (i.e., \(\:\left[0\:0\:1\right]\) , \(\:\left[1\:0\:1\right]\) , and \(\:\left[1\:1\:1\right]\) ) using molecular dynamics (MD) simulations. Microstructural evolutions and mechanical responses are analyzed. Results indicate that different orientations promote transformation into martensitic variants with greater atomic-scale transformation strain, resulting in larger phase transformation strains in the stress-strain responses. Subsequently, microstructure compatibility is studied. Patterns after transformation are classified into three types: parallel twins, twin-twin domains, and multiple-twin domains. The specific patterns formed depend on both loading mode and crystal orientation. Further analyses indicate that: (1) all the interfaces obtained in this study satisfy their corresponding twinning equations; (2) the global compatibility analysis shows the [1 0 1] compression model’s cross twinning matches one ideal case, while the [1 1 1] tension model’s triple junction corresponds to four possible cases. This work provides novel insights into microstructure compatibility in differently oriented NiTi single crystal, enhancing understanding of their phase transformation processes.