We report herein a detailed study on the influence of microwave-assisted hydrothermal (MAH) treatment time on both long and short range structures around Ti atoms of SrTiO3 powders. Few studies have been carried out on short-order structural properties as well as the relationship between the local order and the SrTiO3 photocatalytic properties. We use X-ray diffraction to determine the long-range structure, while the local environment around the Ti atom is probed with X-ray absorption spectroscopy and the vibration frequencies are investigated by Raman spectroscopy. The faster crystallization of SrTiO3 powders provided by the MAH system resulted in large distortions of Ti-O bond lengths which remain unchanged even for a longer MAH treatment time. Despite the long-range structure being associated with ideal TiO6 clusters, X-ray absorption spectroscopy measurements identified the presence of undercoordinated TiO5 clusters. Compared with the reference bulk SrTiO3, the hierarchical SrTiO3 cube-like shape showed enhanced photocatalytic activity, which was associated with the presence of these TiO5 clusters. Field emission scanning electron microscopy (FE-SEM) revealed that the superstructures based on a cube-like shape are formed by an assembly process, becoming well defined as a function of MAH treatment time.