A novel micro heat sink applying the jet-impingement and cross flow is proposed to dissipate the heat from the electrical devices. Six hotspots of 2 mm × 2 mm are positioned on a flat plate of 25.4 mm × 25.4 mm. The area of flat plate except the hotspots is provided a constant heat flux of 20 W/cm2 as background heating source among cases. Four heat fluxes from 40 to 100 W/cm2 on the hotspots are tested to simulate the different operation conditions. The cross flow is used to remove the background heat flux and jet flow is supplied into the swirl microchannel, located at the right top of hotspot, to dissipate the large heat flux from hotspots. The channel depth is 0.5 mm and the width of swirl microchannel is 0.38 mm. The cross flow and jet flow velocity vary from 0.1 m/s to 0.5 m/s and from 0.5 m/s to 2 m/s, respectively. The effects of cross flow and jet flow on the cooling performance are investigated by numerical simulation. The local heat transfer coefficient and Nusselt number are calculated to evaluate the cooling performance of proposed micro heat sink for the targets of low maximum temperature, temperature gradient and pressure drop. The results show that the maximum temperature of the proposed design occurred at the outlet is approximately 65 °C among tested cases. The corresponding pressure drop is 5.5 kPa. The overall thermal resistance reaches as small as 0.23 K/W.