A mild and simple bio-inspired route was successfully developed to synthesize biomorphic metal oxides with hierarchical structures assembled by nanocrystallites. The biomaterials eggshell membrane (ESM) was used as the template in the synthesis process. Based on the directing and capping functions of ESM biomacromolecules for oxide nanocrystallites, the conformation transformation of the natural ESM was achieved to construct 3D interwoven porous ceramic materials. In addition, these building units nanocrystallites exhibited diverse morphologies and had a narrow size distribution with an average crystallite size of 5.4 nm for ZnO, 9.5 nm for Co3O4, and 11 nm for PdO, respectively.