Surface structures of SrTiO₃(001) have been studied by using scanning probe microscopy (SPM) and density functional theory (DFT) calculations. We observed several defective surface structures with true atomic resolution. It is found that all the defects are terminated by (001), (100) and (010) microfacets of TiO₂ plane. We propose microfaceting TiO₂ termination with Sr adatom models. The formation of the various types of defects is driven by the changes of the surface stoichiometry depending on surface preparations.