Rare-earth pyrochlores, commonly exhibiting anomalously low lattice thermal conductivities, are considered as promising topcoat materials for thermal barrier coatings. However the structural origin underlying their low thermal conductivities remain unclear. In the present study, we investigated the phonon properties of two groups of RE pyrochlores, Ln2Zr2O7 (Ln = La, Nd, Sm, Gd) and Gd2T2O7 (T = Zr, Hf, Sn, Pb) employing density functional theory and quasi harmonic approximation.Through the relaxation time approximation (RTA) with Debye model, the thermal conductivities of those RE pyrochlores were predicted, showing good agreement with experimental measurements. The low thermal conductivities of RE pyrochlores were shown to largely come from the interference between the low-lying optical branches and acoustic branches. The structural origin underlying the low-lying optical branches was then clarified and the competition between scattering processes in transverse and longitude acoustic branches was discussed.