In this work, first-principles calculations based on density functional theory within the generalized gradient approximation (GGA) parameterized by Perdew, Burke, and Ernzerhof (PBE) are used to investigate dominant defects in Co-doped SrTiO3 as well as other dominant native defects in SrTiO3. Our calculations revealed that CoTi defect in 1- charge state is the most dominant defect under Ti-poor condition. This indicated that Co atom is likely to substitute on the Ti site to form the CoTi defect in the Co-doped SrTiO3 system whereas the VO defects in 2+ charge state is likely to form in SrTiO3 under O-poor condition due to its comparatively low formation energy. It means that the VO defects is unavoidable in SrTiO3 under this condition. Regarding Sr-poor condition, the dominant defects at the pinned Fermi-energy are VO and VSr defects in 2+ and 2- charge state, respectively. Our calculations show that the CoSr defect is unlikely to form in Co-doped SrTiO3 under all growth conditions. In addition, we found that Coi-VSr complex defect is more likely to form in Co-doped SrTiO3 than isolated defect of CoSr. To be confirmed, simulated Co K-edge x-ray absorption near-edge spectroscopy (XANES) spectrum of CoTi defect is in consistent with the measured XANES spectrum of 12.5% Co-doped SrTiO3 sample annealed in air. The effect of defect nature and formation on the functional properties of Co-doped SrTiO3 was revealed that Co preferentially substitutes at the Ti site (CoTi), consistent with XANES analysis, while oxygen vacancies are unavoidable under O-poor conditions. These defects significantly influence material performance: CoTi narrows the band gap, enhancing optical absorption; oxygen vacancies and mixed Co valence states promote room-temperature ferromagnetism; and vacancy-mediated dipoles improve dielectric permittivity. The combined theoretical and experimental results establish defect engineering as a key route for tuning multifunctional properties of SrTiO3-based oxides.