Single crystalline samples of magnesium aluminate spinel (MgAl2O4), <100> oriented, were irradiated at 100 K and 670 K with 370-400 keV Xe ions to doses of (1-2)x1016 Xe/cm2. The microstructures of irradiated samples were subsequently examined by cross-sectional transmission electron microscope. A uniform layer of amorphous phase was observed on the surface of spinel irradiated at 100 K. At the end of the damage range underlying the amorphous layer, a disordered transition layer resided on the undamaged substrate. Both high resolution electron microscopy and microdiffraction revealed that the transition layer retained single crystallinity with epitaxial relationship to the underlying substrate. However, the intensity of <220> reflections in the transition layer was significantly weaker than that of the undamaged spinel. No evidence of amorphization was found in the spinel sample irradiated at 670 K to a dose of 2x1016 Xe/cm2. The <220> reflections exhibit only limited diminution in the heavily damaged region. The observation of reduced intensity of <220> reflections or absent reflections suggests that spinel experiences a structural transition from its original cubic phase (a=0.808 nm) to a new cubic phase (a=0.404 nm). A transition sequence from the original phase to a metastable phase and then to an amorphous phase has been observed. The temperature dependence of metastable and amorphous phase formation has revealed that the accumulation efficiency of cation disorder decreases with increasing irradiation temperature due to the enhancement of interstitial-vacancy recombination.