We report on the phase transformation of hydrogen titanate (H2Ti3O7) nanowires induced by 50 keV N+ ion irradiation at room temperature with fluences of 1 × 1015 ions/cm2 and 1 × 1016 ions/cm2, respectively. Using transmission electron microscopy, the internal structure of the ion irradiated nanowires is analyzed. At low fluence, a transformation from crystalline H2Ti3O7 to amorphous TiO2 is observed. However, at higher fluence, a remarkable crystalline-amorphous TiO2 core-shell structure is formed. At this higher fluence, the recrystallization occurs in the core of the nanowire and the outer layer remains amorphous. The phase transformation and formation of core-shell structure are explained using the thermal spike model, radiation enhanced diffusion, and classical theory of nucleation and growth under non-equilibrium thermodynamics. X-ray photoelectron spectroscopy and Raman scattering reveal further insight into the structure of the nanowires before and after ion irradiation.