In this study, hydrogenation of carbonyl sulfide (COS) has been investigated over nano-catalyst derived from single-crystalline Co 3O 4 nanocrystals with different morphology. Co 3O 4 nanocrystals, i.e. nanorods and nanopolyhedra, are synthesized by a facile ethylene glycol route and subsequent thermal process. After in situ presulfidation, hydrodesulfurization (HDS) of COS is conducted on these unsupported catalysts in the temperature range of 150–300 °C. Compared with the sulfided nanopolyhedra, the catalytic activity of the sulfided nanorods is much higher especially at low temperature of 200 °C. Surface areas, crystalline phase and particle size distributions of the nanocrystals are determined by Brunauer–Emmet–Teller method, X-ray diffraction and transmission electron microscopy, respectively. It is shown that the catalytic properties of the as-prepared nanocrystals are dependent on the nature of their surface structure, and the crystal plane of Co 3O 4 plays an important role in determining its degree and easiness of presulfurization and consequently HDS performance for COS. The shape-controlled synthesis of nanocrystals may be an effective means for promoting reactive activities for HDS catalysts.