Unique three-dimensionally (3D) ordered nanoporous calcite single crystals have been fabricated by exploiting the "amorphous to crystalline" strategy in combination with the colloidal crystal templating method. It was revealed that the surface-functionalized template and the vacuum-assisted filtration process were essential for the complete template replication. Such a bio-inspired strategy may suggest a general strategy for the fabrication of novel functional single-crystalline materials with 3D ordered nanopatterns.