In order to investigate the phonon scattering mechanisms in double-filled skutterudites, the low-temperature lattice thermal conductivities of Ino.lYbyCO4Sb12 were measured and analyzed based on the Debye model. The eingenmode frequencies of In and Yb were obtained from low-temperature specific heat capacity analysis. It is found that filling these two types of guest atoms with different eingenmode frequencies into the voids in skutterudites could introduce strong point defect and resonant scattering to lattice phonons, thus lead to significant decrease in the lattice thermal conductivity.