Ion irradiation plays an important role to tailor the microcrystalline structure and the corresponding magnetic anisotropy by high local energy deposition and defect accumulation. In the present work, we have investigated the effects of nuclear energy loss and electronic energy loss on the phase transformation and magnetic anisotropy of thin polycrystalline Co films. As-deposited film shows polycrystalline behavior with twofold uniaxial magnetic anisotropy, characteristic to hcp-Co film. 320 keV Au ions induce phase transformation from hcp to fcc. Similar phase transformation have been observed in the case of filmirradiated by 120 MeV Au ions. Rate of phase transformation is discussed in terms of electronic and nuclear energy losses and the corresponding changes in the magnetic anisotropic behavior are discussed in the light of uniaxial and fourfold magnetic anisotropy.