In this study, the steepest-entropy-ascent quantum thermodynamics (SEAQT) framework is used to investigate the excitation transfer (ET) dynamics of two-level nanosystems (TLSs), focusing on non-resonant processes that involve a dynamic local phonon system. In contrast to other methods based on Markovian or non-Markovian quantum master equations, SEAQT analysis always guarantees the positivity of the density operators, thus enabling the discussion of both transient and long-term dynamics of nanosystems. The findings of this study demonstrate that the relaxation time of coherent phonons, relative to the Rabi oscillation period in two TLSs, significantly affects the relaxation process of non-resonant ETs. Moreover, the degree of mutual synchronization between ET dynamics of TLSs and local (coherent) phonons can either prolong or shorten the decoherence time, presenting a way to control the coherence in nanosystems and stimulate quantum device applications.