The bcc—hcp structural transition in single crystal iron under 〈001〉 uniaxial strain has been investigated by molecular dynamics simulation. The reversibility and the morphological characteristics are discussed. The stress history indicates a super-elastic deformation in the sample, while the change of temperature shows the heat release during both hcp and bcc nucleation. A laminated structure of bcc and hcp along {011} planes is obtained, where the phase boundaries for the bcc to hcp and hcp to bcc transition are found along the same plane, implying the memory effect of morphology. Stacking faults (fcc) can be formed at the interface between hcp nuclei. For the bcc to hcp transition, we observed the mergence of the stacking faults in an hcp grain and the position adjustment between hcp grains. No migration of stacking fault is found during the hcp to bcc transition. In addition, the bcc—hcp transition structure is analyzed by the radial distribution function.