A class of nanostructured surface phases on SrTiO3(001) is reported and characterized through atomic-resolution scanning tunneling microscopy and Auger electron spectroscopy. These surface phases are created via argon ion sputtering and UHV annealing and form close-packed domains of highly ordered nanostructures. Depending on the type of nanostructures present, the domain ordering exhibit either (6 x 2), (9 x 2), (12 x 2), (6 x 8), or ( 7 x 4) surface patterning. The nanostructures are composed of TiO2-derived complexes surrounded by a TiO2 surface termination. Such surface ordering phenomena introduce another level of complexity in the chemistry of perovskite oxide surfaces and provide a basis from which potential photocatalytic and molecular-ordering applications may be developed.