Power electronic equipment and the accompanying thermal management system inevitably suffer vibration environments in the aerospace and vehicle fields. Discontinuous mating surfaces between thermal management components are vulnerable to vibration conditions on account of dramatic vibration response differences, seriously degrading the heat dissipation efficiency and inducing overheat of electronics. To avoid unpredictable heat collapse, it is indispensable to establish a numerical prediction method for the contact heat transfer characteristics between solid–solid mating surfaces. A mechanical-thermal sequential coupling approach is developed to clarify the real contact state and heat transfer characteristics of the contact interface, which is effectively verified by experiments. The research indicates that the contact heat transfer under vibration depends on the real contact area in the mating interface. The thermal contact conductance shows thermal fluctuation under vibration conditions, exhibiting the vibration frequency-dependent periodic fluctuation. Compared to triangular and sinusoidal wave vibration, trapezoidal wave leads to more drastic temperature fluctuation of the heat source. The results provide valuable guidance for the optimization design of thermal management systems and the expansion of the application field.