Next to electrons, phonons play a major role for the behavior of nano-scale devices. Additionally, phononics and nano-mechanics offer the possibility to steer and manipulate phonons. Hence, a more detailed understanding of phonon dynamics is required. Using an auxiliary-mode approach, which has successfully been applied for the case of electrons, we present a method to describe time-dependent phonon transport based on the time-dependent Green’s function formalism. This allows us to study local vibrations which are driven by time-dependent temperature differences between heat reservoirs.