Audible sound waves have the advantages of non-contact and strong controllability, which can effectively enhance air heat transfer. Numerical models for the incidence of sound waves and field synergy analysis were established, and the transient flow and heat transfer characteristics in an air-to-air heat exchanger were explored to reveal the influence of sound waves on transient heat transfer characteristics. The results show that the flow structure is changed under high amplitude sound waves (140 dB), and the vortex behind the heat pipes disappears and re-generates, indicating that the synergy degree will change significantly in this region. The velocity, synergy angle, and heat flux fluctuate periodically under the effect of sound waves, and the time-averaged velocity changes slightly while the time-averaged synergy angle and heat flux vary with sound pressure levels (SPLs). The synergy angle on the cold and hot sides is less and larger than 90°, and the location on the heat transfer surface with higher heat flux has a better synergy degree on both sides. Besides, the variation of volume-averaged synergy angle (θ_tave) on the hot side is more consistent with that of heat flux in one acoustic period, which means that the synergy degree in heat pipes affects the heat transfer performance more. When the SPL increases from 0 dB to 140 dB, the θ_tave on the cold and hot sides decreases and increases by 3.4% and 5.9%, and the heat flux increases by 31.5%. This research can provide guidance for the optimization of air-to-air heat exchanger performance using sound waves.