Thermal management is crucial for the proper functioning of a system whether it is in electronics, process industry, automobile, and renewable devices. Micro-channel heat exchanger has proved to be efficient in heat ejection from renewable systems due to high heat transfer surface to volume ratio. This study focuses on evaluating the cooling performance of straight, wavy, and dual wavy Micro-Channel Heat Exchanger by modelling the heat transfer model in ANSYS Fluent. The incompressible fluid is considered in the laminar regime using alumina-based nanofluids with 1%, 3%, and 6% concentration. The solution is computed by selecting SIMPLE pressure-velocity coupling scheme with second-order momentum and energy discretization. Nusselt number, pressure drop, base temperature, and Thermal Performance Factor (TPF) are used as performance parameters for comparing nanofluids performance at Reynolds number range of 100–900. For straight, wavy, and dual wavy model heat transfer, as well as pressure drop, increased with Reynolds number. It is observed that wavy and dual wavy channels compared to straight channel improved convective heat transfer due to the formation of secondary vortices at the curved section. Dual wavy with wavy base and flat base wall showed highest Nusselt number increase of more than double when compared with straight channel of equal concentration. For 6% nano particles addition in all channels, on average both dual wavy channels showed highest improvement of 8% when compared with 0% concentration channel. Dual wavy channel with a flat base and wavy base reduced the base heater temperature by 10 °C and 9 °C compared to the straight channel. A maximum Thermal Performance Factor of 2.2 is achieved for dual wavy channel with a wavy base configuration with 6% nanoparticles.