The processes for the synthesis of polymers in a mesocrystal structure were studied for understanding of the mechanisms. The mesocrystal structure has the nanoscale pores between the unit crystals for incorporation of guest molecules. The monomers can be incorporated and polymerized in the nanospace of the mesocrystals. In the present work, a sea urchin spine and poly(3,4-ethylenedioxythiophene) (PEDOT) were adopted as a model of the original mesocrystal and replicated polymer material, respectively. A sea urchin spine, as an original material, has the hierarchical architectures based on the mesocrystal structure consisting of the oriented carbonate nanocrystals. The monomers were introduced in the nanoscale pores. The composite of the original carbonate and PEDOT was obtained after the incorporation and the polymerization. After dissolution of the original carbonate, the resultant PEDOT architecture showed the hierarchical morphologies similar to those of the original sea urchin spine. The morphology replication processes were compared with those of the different polymers. The important factors for the morphology replication are studied. The present work suggests that the approach can be applied to morphogenesis of a variety of polymer materials.