The microchannel heat sink (MCHS) is used to remove the high heat flux from the miniaturized devices to keep the temperature below the critical bound. It is also necessory to maintain the high heat transfer rate, uniform temperature distribution, less pumping power, maximum thermo-hyraulic performance, etc. The introduction of micro-structure is one of the important techniques to enhance the performances of MCHS. However, the effect of the various shapes and arrangements of the micro-structures also have a significant role which need to be discovered. The present computational study predominently concentrates to analyze the performance of MCHS with the different shapes ofmicro-structures. The study identified that the heat transfer performance and the pressure drop is increased when the single larger micro-structure split into the number of smaller micro-strucures and equally distributed throughout the channel. However, the cross-section of micro-structure also influences the performance of MCHS. The gradual change in the cross-sectional area of the micro-structure along the flow direction causes the pressure drop reduction.