Grain boundary (GB) phase transformations often occur in polycrystalline materials while exposed to external stimuli and are universally implicated in substantially affecting their properties, yet atomic-scale knowledge on the transformation process is far from developed. In particular, whether GBs loaded with defects due to treatments can still be conventionally considered as disordered areas with kinetically trapped structure or turn ordered is debated. Here we combine advanced electron microscopy, spectroscopy and first-principles calculations to probe individual TiO2 GB subject to different atmosphere, and to demonstrate that stimulated structural defects can self-assemble at GB, forming an ordered structure, which results in GB nonstoichiometry and structural transformations at the atomic scale. Such structural transformation is accompanied with electronic transition at GB. The three-dimensional transformations afford new perspectives on the structural defects at GBs and on the development of strategies to manipulate practically significant GB transformations.