Filled skutterudite is a typical thermoelectric material with high thermoelectric figure of merit at intermediate temperatures. One of the important features is the low lattice thermal conductivity (L) caused by the low frequency vibrations of filler atoms in the oversized void cages. In the past decades, it has been still under debate whether the underlying phonon scattering mechanism should be considered to be resonant scattering or enhanced three-phonon process. To clarify the role played by the filler atoms in reducing the lattice thermal conductivity, we study the microscopic dynamical process of filler and related interactions by means of ab initio molecular dynamics (AIMD) and temperature dependent effective potential (TDEP) technique. Firstly, we simulate the dynamical trajectories of fully filled skutterudite YbFe4Sb12 at different temperatures through AIMD. In this approach, the nonlinear guest-host interactions at finite temperatures are taken into consideration naturally from dynamical trajectories. Then, we extract the effective temperature-dependent harmonic and anharmonic interatomic force constants (IFCs) by TDEP method through the statistical analyses of both trajectories and forces. The atomic participation ratios and lifetimes of phonon modes are calculated based on the effective IFCs. The results demonstrate that the local vibration modes of Yb couple with acoustic branches and reduce the lifetimes of the lattice phonons significantly. However, the calculated L, which is on the assumption that the filler interacts with lattice phonons through three-phonon collision, still deviates from the experimental result. In order to rationalize the discrepancy, we analyze the correlation properties between different Yb atoms by velocity coherence in atomic dynamical motions. The localized and independent vibration characteristic of Yb is found in this analysis. This implies that the motions of Yb atoms deviate from the periodic and collective vibration excitation paradigm of phonon. Therefore, the mechanism for how filler atoms scatter lattice phonon and enhance thermal resistance is beyond three-phonon scattering process. We thus introduce resonant scattering into the lifetimes of Yb-dominant localized vibration modes, and so-calculated L is in a good agreement with the experimental data. Overall, we come to a conclusion that both the phonon-phonon interaction and the resonant scattering due to the localized oscillators cause the low lattice thermal conductivity of YbFe4Sb12.