Microchannels have many applications in the field of modern technologies. Today, it is necessary to increase the efficiency of these systems due to the increasing rate of thermal loads. Recent researches have shown that liquid flows in the microchannels depend on their size and surface properties. Consequently, there is no symmetric flow condition in a symmetric geometric channel necessarily. In this study, the effect of slip length on the amount of asymmetric heat transfer in a microchannel is investigated numerically. By calculating the parameters such as Nusselt number and local pressure drop coefficient, it is observed that the asymmetric slip flow affects the flow profile and could lead to a decrease or increase in the heat transfer in the microchannel. According to the results, asymmetric slip flow can lead to a 20–40% reduction or increase in the Nusselt number. The most important point in the design of micro-scale asymmetric cooling systems is the increase of slip length at high temperatures.