Hierarchical assembly of hollow microstructures is of great scientific and practical value and remains a great challenge. This paper presents a facile and one-pot synthesis of Cu2O microspheres with multilayered and porous shells, which were organized by nanocrystals. The time-dependent experiments revealed a two-step organization process, in which hollow microspheres of Cu2(OH)3NO3 were formed first due to the Ostwald ripening and then reduced by glutamic acid, the resultant Cu2O nanocrystals were deposited on the hollow intermediate microspheres and organized into finally multishell structures. The special microstructures actually recorded the evolution process of materials morphologies and microstructures in space and time scales, implying an intermediate-templating route, which is important for understanding and fabricating complex architectures. The Cu2O microspheres obtained were used to fabricate a gas sensor, which showed much higher sensitivity than solid Cu2O microspheres.