Nanolayered structural metallic ceramics, MAX phases, possess unique and highly attractive properties, including excellent radiation tolerance for some of them, whereas little is known about the detailed process of irradiation-induced structural transitions. In this study, the microstructural transformations and the stabilities of V2AlC and Cr2AlC induced by 1 MeV Au+ ions irradiation over a wide range of fluences were investigated by grazing incidence X-ray diffraction (GIXRD) and transmission electron microscopy (TEM). GIXRD analyses show different processes of phase transitions and amorphization tolerance under irradiation between these two MAX phases, which are consistent with the selected area electron diffraction (SAED) results and the high-resolution observations. TEM observations reveal that the nanolamellar structures are disturbed and respective phase transitions occur at relatively low fluences, with the formation of stacking faults. As the fluence increases, Cr2AlC becomes completely amorphous, while V2AlC are gradually transformed into face-centered cubic (fcc) structure from the original hexagonal close-packed (hcp) structure without amorphization, indicating that V2AlC is more tolerant of irradiation than Cr2AlC. Based on the phase contrast images and the electron-diffraction pattern (EDP) simulation of the microstructures, mechanisms of the phase transitions of V2AlC and Cr2AlC are proposed and the difference of the irradiation tolerance between them is discussed.