Ordered domains are utilized to construct new nanostructures, i.e., multishell intermetallic onions, which are formed by symmetrical configuration of ordered domains. Through density-functional theory calculations, we have shown that the energy penalties for introducing antiphase boundaries into the nanoparticles are small in some alloy systems compared to typical surface energies, making it feasible to prepare intermetallic onions by tuning surface energies. The unique surface atomic arrangements would provide opportunities for developing novel materials like efficient catalysts.