Ceria nanorods enclosed with {110}/{100} planes and ceria nanocubes with {100} planes have been successfully prepared using a homemade microfluidic system in a continuous, ultrafast and shape-controllable manner. Only 8 min of reaction time are needed rather than days to synthesize ceria nanostructures in the traditional batch hydrothermal method. During the synthesis, reaction temperatures and base concentration have been demonstrated as the key factors responsible for the shape evolution. Accordingly, a morphological phase diagram was determined. In addition, polyvinylpyrrolidone was introduced to realize the transformation from ceria nanorods to nanocubes under unfavorable hydrothermal conditions. Catalytic performance of different CeO2 architectures was also examined in decomposing hydrogen peroxide and a reactivity trend (nanoparticles < nanorods < nonocubes) was observed. This is assumed to be related with different surface oxygen vacancy amounts as a result of {110}/{100} preferential planes, as confirmed by X-ray photoelectron spectroscopy and Raman analyses as well as density functional theory (DFT+U) calculations.