Single-crystalline porous CeO2 nanocrystals, with sizes of 20 nm and pore diameters of 1–2 nm, were synthesized successfully using a hydrothermal method. Using electron tomography, we imaged the three-dimensional structure of the pores in the nanocrystals and found that the oriented aggregation of small CeO2 nanoparticles resulted in the growth of CeO2 nanocrystals with an irregular truncated octahedral shape and pores extending along the 110 directions. Oxygen vacancies were found on the crystal surfaces and internal walls of the pores by scanning transmission electron microscopy and electron energy-loss spectroscopy. The oxygen vacancies might play an important role in oxygen diffusion in the crystals and the catalytic activities of single-crystalline porous CeO2 structures.