The compression-induced structural transition (ST) and grain refinement of BCC Fe nanowires have been investigated based on atomistic simulations. It is found that high strain rate compression can cause nanowires to reach higher pressures and meet ST conditions, and the threshold stress of ST is found to be much lower than that of bulk materials. Thus, the compression process of nanowires at high strain rates includes elastic deformation, ST and its reverse process, grain refinement, and buckling instability. The occurrence of grain refinement is due to the fact that after undergoing ST and its reverse process, the (001) cross section of the nanowire can be transformed into different (111) planes. Furthermore, the dependence of stress threshold and nucleation structure on strain rate is revealed. When the strain rate increases to a certain threshold, HCP nucleation is found to occur on the side surface of the nanowire, but its reverse process will quickly occur due to the pressure release on the side. With the strain rate increase, the stress threshold of ST no longer satisfies a constant power-law change, and the power-law index will increase. When the strain rate exceeds 5 × 1010 s−1, the elastic deformation prior to ST also exhibits strong nonequilibrium characteristics, causing a sharp increase in the number of HCP nuclei. Especially, the nanowires will ultimately be in a disordered state, rather than a nanocrystalline structure. Also, the cylindrical and prismatic nanowires are both considered to understand the influence of boundary morphology, and the differences in nucleation and the similarity in deformation are explained. Note that, as the strain rate increases, the cylindrical nanowires undergo HCP nucleation directly, while the prismatic nanowires undergo significant twinning deformation first.