Recently, a new anti-irradiation mechanism relying on reversible disorder-ordering transition of coherent nanoparticles was discovered, which significantly improves the microstructural stability and void swelling resistance of metallic materials. However, the factors that govern the outstanding stability and superb radiation tolerance are still not clear. Here, two kinds of FeCrAl alloys were designed, each strengthened by a different type of coherent phase: L21-ordered Fe2AlV and B2-ordered Ni (Al, Fe). It was observed that the two alloys exhibited disparate responses to high-dose ion irradiations at elevated temperatures. The L21-Fe2AlV precipitates were found to be completely dissolved after 50 dpa of ion irradiation at 500–600 °C, whereas the B2-NiAl precipitates remained stability even after 200 dpa irradiation. This research challenges the conventional wisdom that the stability of nanoparticles is governed by the balance between radiation-enhanced coarsening and radiation dissolution. Instead, it demonstrates the re-nucleation and subsequent interface-controlled solute reshuffling processes govern the stability of coherent chemically-ordered nanoparticles under radiation at high temperatures. We demonstrate that the low interfacial energy, which is related to both the simply chemically-ordered lattice structure and low lattice misfit interface, is crucial for enabling such short-range elemental reshuffling process to repeatedly form nanoprecipitates that cannot be suppressed by radiation.