Photonic materials for high-temperature applications need to withstand temperatures usually higher than 1000 °C, whilst keeping their function. When exposed to high temperatures, such nanostructured materials are prone to detrimental morphological changes, however the structure evolution pathway of photonic materials and its correlation with the loss of material's function is not yet fully understood. Here we use high-resolution ptychographic X-ray computed tomography (PXCT) and scanning electron microscopy (SEM) to investigate the structural changes in mullite inverse opal photonic crystals produced by a very-low-temperature (95 °C) atomic layer deposition (ALD) super-cycle process. The 3D structural changes caused by the high-temperature exposure were quantified and associated with the distinct structural features of the ceramic photonic crystals. Other than observed in photonic crystals produced via powder colloidal suspensions or sol-gel infiltration, at high temperatures of 1400 °C we detected a mass transport direction from the nano pores to the shells. We relate these different structure evolution pathways to the presence of hollow vertexes in our ALD-based inverse opal photonic crystals. Although the periodically ordered structure is distorted after sintering, the mullite inverse opal photonic crystal presents a photonic stopgap even after heat treatment at 1400 °C for 100 h.