The present study explores the role of Ti ion implantation in structural phase transition in TiO2 thin films. Raman and TEM results reveal that after implantation Rutile phase in films increases at the expense of Anatase nanostructures. Though the as-deposited films display the presence of bigger anatase nanoparticles, after implantation, predominantly phonon confined smaller (∼ 8 nm in size) anatase nanostructures are observed. GIXRD and Raman results further reflect presence of a critical fluence, 1 × 1013 ions/cm2, where the initial transformation from anatase to Rutile phase is observed. The role of Oxygen vacancies, in this transformation, has been explored here by XPS. Modifications in UV–Vis and Bandgap results show rich behavior which also reflects phase transformation at the critical fluence. Results further indicate that the phase transition gets first initiated deeper in the film and later on the surface. Interestingly, aggregation of larger Anatase nano-particles appears to be responsible for the structural transformation as observed here.