We report the evolution of structural distortions on the pulsed laser deposited SrTiO3 (STO) thin films irradiated by 1 MeV Ar ion beam and their response in the electrical and thermoelectric properties correlated with their electronic structures. The structural studies reveal a modification in the crystalline nature resulting in the synergistic enhancement of resistivity and the Seebeck coefficient due to ion irradiation-induced oxygen vacancies and augment the power factor to ∼17 μW m−1K−2, which is 2.5 times higher than the pristine STO. An in-depth analysis of the conduction mechanism using various theoretical models implies the role of band conduction and Mott-variable range hopping. Further, the changes in the local electronic structures are reflected in the variation in the Ti–O bond length and the density of unoccupied states that alter the spectral intensities and chemical shifts and are responsible for the observed enhancement in the thermoelectric properties. The above results indicate the significance of the ion beams to tune the electrical and thermoelectric properties.