The effects of flexibility in the homogeneous nucleation processes of UF6 and SF6 molecules from vapor phase were investigated by classical molecular dynamics (MD) simulations. We performed MD simulations using a flexible-molecule model and compared the results with those obtained from a rigid-molecule model. We took into account the flexibility of molecules in MD simulations by a harmonic intramolecular potential. We found that the nucleation rate in the flexible model of the UF6 molecule was about twice as large as that in the rigid model of UF6. This acceleration in nucleation rate was attributed to the flow of the condensation heat into the intramolecular vibrations. On the other hand, the nucleation rates in rigid and flexible models of SF6 were almost the same because the flow of the condensation heat into the intramolecular vibrations in the flexible model of SF6 was negligibly small. In order to confirm the reliability of the classical intramolecular vibrational model in the present work, we estimated the intramolecular vibrational relaxation times of the flexible UF6 and the flexible SF6 molecules in the gas phase using the same MD simulation technique as used for the nucleations. The intramolecular vibrational relaxation times obtained from the MD simulations were in good agreement with those from the experimental data in cases of both UF6 and SF6 molecules.