We report a structural transition found in Ca10(Ir4As8)(Fe2-xIrxAs2)5, which exhibits superconductivity at 16 K, with a layer of divalent iridium coordinated by arsenic in between Fe2As2 layers. The c-axis parameter is doubled below a structural transition temperature of approximately 100 K, while the tetragonal symmetry with space group P4/n (No.85) is unchanged at all temperatures measured. Our synchrotron x-ray diffraction study clearly shows displacements along the z-direction occur in half of the iridium sites, resulting in a complex orbital ordering pattern. Combining our theoretical calculation of the 5d orbital energies with structural data, we propose the iridium orbital crossover transition between the dxy and dz2 orbitals.