The rare earth intermetallic compounds, RFe2Zn20 （R　represents rare earth）, have become one of hot spots in research field due to their excellent magnetic properties with lower concentration of rare earth atoms. The addition of quaternary could influence the structural properties. The crystal structures of ternary RFe2Zn20 and site preferences of quaternary RFe2Zn20-xInx compounds are investigated by using interatomic potentials based on the lattice inversion technique. The calculated results show that the lattice constants and cell volumes of RFe2Zn20 decline linearly with atomic weight of rare earth increasing and the linear relation is independent of whether the quaternary element is added into the compounds. The In atoms substituted for Zn atoms preferentially occupy 16c site and then 96g site, without 48f site. The sequence of site preference is coincident with the measurements and the analyses from interatomic potentials.