We have determined the crystal structure of U-phase, which is one of the calcium-aluminate layered double hydroxides (Ca–Al LDHs). Based on X-ray powder diffraction data, we derived the hydrogen-free structural model with space group R3 and hexagonal unit-cell dimensions a = 0.99404(1) and c = 3.00791(4) nm. The location of hydrogen sites was determined by calculation methods. The final structural model, with structural formula [3Ca₂Al(OH)₆][Na(H₂O)₆(SO₄)₂‧6H₂O] (Z = 3, a = 0.99372 and c = 2.82658 nm), was composed of [Ca₂Al(OH)₆]⁺ layers and [Na(H₂O)₆(SO₄)₂‧6H₂O]^3– interlayers. They were alternately stacked in c-axis direction and connected by hydrogen bonds to build the overall structure. The positions of Ca²⁺ in Ca(OH)₆⁴⁻ octahedra were significantly shifted from the centroids of octahedra. Considering the coordination environment of divalent cations in Mn²⁺-Al LDH and Fe²⁺-Al LDH, the remarkable displacements of Ca²⁺ sites in the relevant octahedra would be one of the common structural characteristics of Ca–Al LDHs.