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• Hotspot heat transfer using a microchannel pin-fin hybrid heat sink is investigated numerically. • Pin-fin shape, pin-fin angle, wall wave amplitude, Reynolds number and hotspot heat flux are investigated. • Rectangular pin-fin with rounded edges have better thermal performance than NACA 0024 airfoil. • Increasing the NACA 0024 airfoil angle increases the heat transfer and consequently leads to decrease in hotspot temperature. • By increasing the airfoil pin-fin angle, MATD improves in the base of heat sink and hotspot. In the present study, numerical investigation of hotspot heat transfer in a microchannel pin-fin hybrid heat sink is accomplished. The proposed heat sink consists of 20 microchannels at background zone and 143 pin-fins at hotspot zone. Therefore, the effect of parameters including geometrical properties (pin-fin shape, pin-fin angle and microchannel wall wave amplitude), Reynolds number and hotspot heat flux on different decisive parameters of heat sinks are investigated. Parameters such as average pressure drop, pumping power, mean absolute temperature difference (MATD) at background zone, MATD at hotspot zone and thermal resistance are considered as performance parameters. The results show that rectangular pin-fin with rounded edges have better thermal performance than NACA airfoil. Besides, increasing the NACA airfoil angle increases the heat transfer and consequently leads to decrease in hotspot temperature. Also, numerical results show that increasing the wall wave amplitude increases the heat transfer rate. [ABSTRACT FROM AUTHOR]