Revealing the mechanism of phase selectivity can provide guidance for controlling crystals with certain phases for special properties. In the present work, nanocrystals of about 2–4 nm diameters with a B2 structure (thermodynamic metastable phase) are generated from CuZr glassy fiber by applying tensile stress at ambient temperature. By combining the ab initio calculations with the molecular dynamics simulations, the stabilities of B2 austenite and B19′ martensitic phases under applied tensile stress are compared, and the phase transformation mechanism is revealed. The results show that the B2 structure has a bigger attractive basin, and the phase transition could occur with a larger applied stress during the deformation. Therefore, insights into the higher symmetric B2 nanocrystal with selective nucleation driven under directional stress are provided.