Nanocrystalline zirconia has recently attracted extensive research interest due to its unique mechanical, thermal and electrical properties as compared with bulk zirconia counterparts, and it is of particular importance for controlling the phase stability of different polymorphs (amorphous, cubic, tetragonal and monoclinic phases) in different size regimes. In this work, we performed ion beam bombardments on bilayers (amorphous and cubic) of nano-zirconia using 1 MeV Kr2+ irradiation. Transmission electron microscopy (TEM) analysis reveals that amorphous zirconia transforms to a tetragonal structure under irradiation at room temperature, suggesting that the tetragonal phase is more energetically favorable under these conditions. The final grain size of the tetragonal zirconia can be controlled by irradiation conditions. A slower kinetics in the grain growth from cubic nanocrystalline zirconia was found as compared with that for the tetragonal grains recrystallized from the amorphous layer. The radiation-induced nanograins of tetragonal ZrO2 are stable at ambient conditions and maintain their physical integrity over a long period of time after irradiation. These results demonstrated that ion beam methods provide the means to control the phase stability and structure of zirconia polymorphs.