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In this paper, a three-dimensional solid–fluid conjugate model coupled with a simplified conjugate-gradient method was employed to optimize the performance of double-layered microchannel heat sinks. Channel number, channel width, bottom channel height, and bottom coolant inlet velocity were selected as search variables to achieve the optimal heat sink performance. Firstly, two single-objective optimizations based on different objective functions (one is the maximum temperature change on the bottom wall ΔT_w,b and the other is the overall thermal resistance R) were performed at a constant pumping power. Subsequently, the effects of total pumping power on the optimal ΔT_w,b and R were analyzed, and the optimal search variables at various pumping powers were obtained. For single-objective optimization with the objective function of ΔT_w,b, ΔT_w,b is respectively decreased by 6.01, 5.29, and 2.99 K when …