A nanoscale hierarchical dual-phase structure is reported to form in a nanocrystalline NiFeCoCrCu high-entropy-alloy (HEA) film via ion irradiation. Under the extreme energy deposition and consequent thermal energy dissipation induced by energetic particles, a fundamentally new phenomenon is revealed, in which the original single-phase face-centered-cubic (FCC) structure partially transforms into alternating nanometer layers of a body-centered-cubic (BCC) structure. The orientation relationship follows the Nishiyama-Wasserman relationship, that is, (011) BCC || (111) FCC and [100] BCC || [ 110] FCC. Simulation results indicate that Cr, as a BCC stabilizing element, exhibits a tendency to segregate to the stacking faults (SFs). Furthermore, the high densities of SFs and twin boundaries in each nanocrystalline grain serve to accelerate the nucleation and growth of the BCC phase during irradiation. By adjusting the irradiation parameters, desired thicknesses of the FCC and BCC phases in the laminates can be achieved. This work demonstrates the controlled formation of an attractive dual-phase nanolaminate structure under ion irradiation and provides a strategy for designing new derivate structures of HEAs.