The site preferences of the rare earth intermetallics Nd6Fe13−xTxSi (T = Co, Ni) are investigated by using interatomic pair potentials which are converted from a lattice-inversion method. Calculation shows that the order of the site preference of Co is 4d, 16k, 16l1, and 16l2 and that of Ni is 16l2, 16l1, 16k, and 4d in Nd6Fe13−xTxSi. Calculated lattice and positional parameters are found to agree with those reported in the literature. Furthermore, the phonon density of states for Nd6Fe13−xTxSi is also evaluated, and a qualitative analysis featuring the coordination and the relevant potentials is carried out.