Hydrogels have been thought to be the material which can provide appealing replacements of biological organisms. Pores of hydrogels synthesized from lyotropic liquid crystalline (LLC) templates were smaller in size and more uniform than those of traditional hydrogels. LLC poly-acrylamide (PAAm) hydrogels were used as the growth media of CaCO₃. After copolymerized with acrylic acid and 2-acrylamido-2-methylpropanesulfonic acid (AMPS), LLC hydrogels were modified with COOH and SO₃H, respectively. The effect of functional groups on the biomimetic mineralization of CaCO₃ was studied. Most of crystals from traditional hydrogels are rhombohedral and could not form aggregates. Only a few could aggregate and have a particular morphology with irregular orientation of subcrystal. Compared with crystals separated from traditional hydrogels, crystals growing in the LLC hydrogels were much more regulated and could form aggregates with particular morphology and regular orientation, that is, face (104) of rhombohedral subcrystals parallel to the surface of the macrocrystals. Modification of COOH and SO₃H groups made CaCO₃ subcrystal align more tightly. COOH had minor influences on the crystal orientation and small modification to the aggregate morphology. SO₃H groups could change the crystal orientation and morphology effectively. The aggregates are pseudo-spherical and the face perpendicularity to the face (104) parallels to the surface of the aggregates.