Abstract: In this paper, the flow and heat transfer characteristics of the unsteady laminar flow developed by sinusoidal change of the inlet velocity in the two structural microchannels were studied by a numerical method. The effects of pulsation frequency, amplitude, and Re on the flow and heat transfer in the microchannel were studied respectively. The research results show that the pulsating flow has little effect on the bottom surface temperature of the rectangular channel and heat transfer in the Re range of 100-400, but it has a significant effect on the microchannel with the triangular reentrant cavities. As the pulsation frequency increases, the bottom surface temperature of the channel increases first and decreases later. It is proved that there is a critical frequency that causes the channel bottom temperature to increase when it is less than that frequency and decreases when it is greater than that frequency. As the amplitude increases, the wall temperature decreases and the heat transfer continues to increase. However, as the Re increases, the effect of pulsating flow gradually decreases. The increase of pulsation frequency and amplitude increases the pressure drop of the microchannel.