In the thermal management of fuel cell vehicles, radiators are subjected to vibrations due to vehicle speed and road surface irregularities. However, there has been no comprehensive study of the impact of these vibrations on the heat transfer performance of radiators. Therefore, this paper employs R141b to conduct three-dimensional transient numerical simulations of flow boiling in small channels under vertical vibrations. The study reveals that the single-phase heat transfer coefficient exhibits periodic variations. At the same vibration frequency, the heat transfer frequency for the vertically oriented heating surface is twice that of the horizontally oriented surface, This is because the thermal boundary layer varies with the vibration velocity. Furthermore, as the frequency increases to 21 Hz, the time-averaged heat transfer coefficient can increase by up to 2.5 times. Following boiling onset, for horizontally oriented heating surfaces, an increase in frequency or amplitude enhances the transient heat transfer performance. Under the conditions of 28 Hz and 5 mm, the heat transfer coefficient can increase by 125.7%. However, for vertically oriented heating surfaces, when the frequency exceeds 14 Hz or the amplitude exceeds 8 mm, the heat transfer performance weakens after 7.143 s due to the promotion of bubble coalescence by the vibrations.