The correlation among composition, structure, chemical bond and thermoelectric property of skutterudites of IrSb₃, Ir₄NdGe₃Sb₉ and Ir₄SmGe₃Sb₉ is studied using SCF-DV-X_α method, one of calculation methods in quantum chemistry. Ir₄NdGe₃Sb₉ and Ir₄SmGe₃Sb₉ are calculated with several models for investigating the "rattling" patterns. The results show that the model with rare earth near to Ge is more stable than that with rare earth near to Sb, and the former is with lower thermal conductivity. The covalent bonds of Ir₄SmNdGe₃Sb₉ are weaker than those of Ir₄SmGe₃Sb₉, and those of Ir₄NdGe₃Sb₉ and Ir₄SmGe₃Sb₉ are both weaker than those of IrSb₃, which is consistent with the experimental result of thermal conductivity.