Phase transformation is rare in pure body-centered cubic (BCC) metals due to the associated high energy barrier. Here, omega (ω) phase transformation in single-crystal niobium (Nb) under compression at 77 K was studied by atomistic characterization and density functional theory (DFT) calculation. The ω phases were found to nucleate preferentially at the boundaries of 112 shear bands, via a sequence of BCC-to-ω structural transformation induced by shear stress. Theoretically, calculations reveal that the formation of a shear transition region can reduce the energy barrier of BCC-to-ω phase transformation. These findings provide insights into the phase transformation involved in the cryogenic deformation of bulk BCC metals.