The invention discloses a three-dimensional structure constructed by using graphene as base units and a preparation method thereof. The graphene three-dimensional structure is formed by stacking and assembling graphene, the shape of the graphene three-dimensional structure is a similar cylinder or a polygonal prism, and the volume of the graphene three-dimensional structure is 0.1-100cm<3>. The graphene three-dimensional structure can contain water, methanol, ethanol, glycol and mixture molecules thereof, and can contain Li<+>, Na<+>, K<+>, Ag<+>, Ca<2+>, Ba<2+>, Mg<2+>, Ni<2+>, Co<2+>, Cu<2+>, Mn<2+>, Cd<2+>, Zn<2+>, Pb<2+>, Pt<2+>, Pd<2+>, Rh<2+>, Al<3+>, Fe<3+>, Au<3+>, Ru<3+> and Pt<4+> metal ions. The graphene three-dimensional structure has rich network space which can be used for filling Ni, Co, Cu, Mn, Fe, Au, Ag, Pt and Ru as well as alloy nanoparticles thereof, can be used for filling polypyrrole, polyaniline, polyacrylic acid, polythiophene, polyacrylamide and polyvinyl alcohol polymers, and can be used for filling protein, amino acid, sugar and enzyme biological molecules.