Shape-specific CeO2 nanocrystals (rods, cubes, spheres and nanoparticles) with well-defined crystal facets and hierarchically porous structure were successfully synthesized and used as model catalysts to study the structure-dependent behavior and reaction mechanism for H2S selective oxidation over ceria-based catalysts. It is deduced that the defect sites and base properties of CeO2 are intrinsically determined by the surface crystal facets. Among the nanocrystals, CeO2 nanorods with well-defined {110} and {100} crystal facets exhibits superb catalytic activity and sulfur selectivity. The high reactivity for H2S selective oxidation is attributed to the high concentration of surface oxygen vacancies which are beneficial for the conversion of lattice oxygen to active oxygen species. Besides, the presence of hierarchically porous structure of CeO2 nanorods hinders the formation of SO2 and sulfate, ensuring good sulfur selectivity and catalyst stability. Through a combined approach of density-functional theory (DFT) calculations and in situ DRIFTS investigation, the plausible reaction mechanism and nature of active sites for H2S selective oxidation over CeO2 catalysts have been revealed.