Modern electronic components and their compact dimensions have led to the miniaturization of the systems and at the same time the development of high-performance devices. The demand for heat flux dissipation also increased with the reducing the size of these devices and reached up to 1000 W/cm2. An effective cooling technique is required for effective high heat flux removal from these devices for their safe and efficient operation. A microchannel heat sink (MCHS) can remove large heat flux from electronic components and high-performance computing devices. Heat transfer and flow behavior in microchannel heat sinks were examined. This work investigates numerical measurement of three-dimensional conjugate heat transfer and fluid flow at MCHS. Two different geometric structures of microfins arranged in MCHS are studied. For case 1, rectangular straight fins are considered, and for case 2, square pin fins are considered. The analysis is performed at different operating input parameters by varying Reynolds numbers and heat fluxes. Case 1 shows a better thermal conduction than case 2, which is improved by increasing the Reynolds number. Case 1 has better cooling and lower wall heating temperature than case 2. Hydraulic resistance for case 1 was higher at a low Reynolds number, which became slightly lower than case 2 on increasing Reynolds number.