Neutron diffraction and pair distribution function studies coupled with Raman spectroscopy have successfully unraveled the detailed oxygen defect structures of ceria nanocubes and nanorods. Two types of defect sites are revealed for the ceria nanocrystals: surface and bulk defects. It is proposed that the surface oxygen defects in both types of CeO2 nanocrystals are predominantly the partially reduced Ce3O5+x, with the bulk defect structures dominated by interstitial Frenkel-type oxygen vacancies. Ceria nanorods possess much higher concentration of surface oxygen defects relative to the nanocubes, albeit with only slightly higher concentration of bulk Frenkel-type oxygen vacancies. Upon annealing the nanorod sample at 600 °C under vacuum (∼10–4 to 10–5 mbar), a partially reduced ceria phase with long-range oxygen vacancy ordering (Ce3O5+x) has been observed experimentally for the first time. This intriguing observation that surface defect phases can take on ordered defect sublattices under certain conditions is of great value in understanding the temperature-dependent catalytic performance of ceria nanocrystals. Furthermore, a drastic decrease of the surface vacancies in the ceria nanocrystals is observed upon exposure to SO2, especially for the nanorods, a likely origin for the sulfur poisoning effect on ceria-based materials. This study suggests that tailoring surface morphology is a promising strategy to control defect properties of ceria nanomaterials. It also provides fundamental insights to stabilize surface oxygen defects in CeO2 nanocrystals to achieve high redox performance under corrosive environments such as under SO2/SOx exposure.