In response to the growing thermal management challenges in the aerospace sector, this paper proposes a microchannel cooling technique based on liquid metals, specifically a gallium-indium-tin alloy. The study investigates the heat transfer performance of this cooling method and evaluates its feasibility and potential applications in aerospace systems. For the same microchannel configuration, at a flow rate of 1–2 L/min, the average heat transfer thermal resistance of liquid metal microchannels is reduced by 28.1% compared to conventional water-cooled microchannels. Structural optimizations are applied to the microchannel design, focusing on the number of channels, inlet flow velocity, channel aspect ratio, and thickness-to-width ratio. Under the optimized configuration, liquid metal microchannels achieve a 26.9% reduction in total thermal resistance, requiring 79.2% fewer channels and operating at 50% lower flow velocity than water-cooled microchannels. Additionally, with the same pumping power, liquid metal cooling results in a 60% reduction in overall thermal resistance and requires 30% fewer channels. These improvements lead to lower processing costs, reduced flow resistance, and enhanced heat dissipation performance. In conclusion, liquid metal microchannel cooling presents a highly effective solution for addressing the extreme thermal environments characterized by high temperatures and high heat flux densities in aerospace applications.