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This study proposes a novel design having dense fins with lesser thickness at the upper layer and comparatively spare fins with greater thickness in the lower layer to further improve the overall thermal performance of a double-layer microchannel heat sink. The design can effectively direct more low temperature fluid flow toward the lower layer to improve heat transfer while the sparse fin structure at low layer can ease pressure drop penalty. At the same time, the thicker fins at the lower layer ensure higher fin efficiency to facilitate high heat transfer. Parametric and detailed analysis is conducted for the proposed double-layer microchannel heat sink in comparison with the traditional one. After optimization, the thermal resistance of the proposed double-layer microchannel heat sink at the same pumping power is found to be reduced by 9.42% when compared to the traditional double-layer microchannel heat sink. Yet at the same Reynolds number, the Nusselt number of the proposed design exceeds the traditional value by 13%.