In this work, fluid flow characteristics, heat transfer performance, and entropy-based performance of the microchannel heat sink (MCHS) are studied critically by introducing micro-structures of different cross-sections inside the channels. A single microchannel (dimensions 0.4 mm x 0.4 mm x 50 mm) embedded on a copper substrate (dimensions 0.7 mm x 0.7 mm x 50 mm) is considered. The analysis has been divided into three different stages. At first, the type of microstructure that improves the fluid flow and heat transfer characteristics has been identified as the micro-ribs placed at the bottom surface of the channel. As this configuration improves the heat transfer coefficient and reduces pressure drop and entropy generation rate, it has been considered for the next analysis. Next, the cross-section of the micro-ribs is optimized by considering the various cross-sections. The aerofoil and reversed aerofoil micro-ribs have been ascertained to be the best possible cross-section of the micro-ribs that improves the performance evaluation criteria of the heat sink nearly 1.4 times with reference to the plain channel. The aerofoil and reversed aerofoil micro-ribs improve heat transfer and reduce the pressure drop respectively. Based on the outcome of these three analyses, a novel arrangement of micro-ribs with twelve aerofoil micro-ribs at the upstream half and twelve reversed aerofoil at the downstream half of the channel has been proposed. The proposed microchannel heat sink can dissipate heat twice the value of a plain microchannel for the same average interface temperature.