A single crystal of Gd⁢Ba⁢Co2⁢O5.47⁢(2) has been studied by means of x-ray diffraction. Below the first-order metal-insulator transition, a continuous transition to a phase with a doubled orthorhombic unit cell is discovered at 𝑇𝐶=341.5⁢(7) by the appearance of very weak superstructure reflections. The critical exponent for the order parameter is found to be 𝛽=0.328⁢(8), indicating an Ising pseudospin ordering in a 3D system. The systematic extinction of the superstructure reflections evidences the crystal symmetry change from 𝑃⁢𝑚⁢𝑚⁢𝑚 to 𝑃⁢𝑚⁢𝑚⁢𝑎, which explains the existence of a spontaneous moment. The integrated intensities are used to calculate the atomic displacements from their positions in the high-temperature phase. The cobalt-ligand distances in the ordered phase are discussed in terms of possible spin-state and/or orbital ordering of Co3+ ions.