The issue of regenerative cooling is one of the most important key technologies of flight vehicles, which is applied into both the engine and high-power electrical equipment. One pattern of regenerative cooling channels is the microchannel heat sinks, which are thought as a prospective means of improving heat removal capacities on electrical equipment of smaller sizes. In this paper, three numerical models with different geometric configurations, namely, straight, zigzag, and sinusoid, respectively, are built to probe into the thermal hydraulic performance while heat transfer mechanism of supercritical methane in microchannel heat sinks for the heat removal of high-power electromechanical actuator is also explored. In addition, some crucial influence factors on heat transfer such as inlet Reynolds number, operating pressure, and heating power are investigated. The calculation results imply the positive effect of wavy configurations on heat transfer and confirm the important effect of buoyancy force of supercritical methane in channels. The heat sinks with wavy channel show obvious advantages on comprehensive thermal performance including overall thermal performance parameter η and thermal resistance R compared with that of the straight one. The highest Nu and average heat transfer coefficient αm appear in the heat sink with zigzag channels, but the pumping power of the heat sink with sinusoidal channels is lower due to the smaller flow loss.