The existing heat transfer technologies suffer from numerous limitations and are poor in high performance and high heat dissipation. Liquid cooling using microchannels and nanofluids work with the increased surface area and minimum thermal resistance. Many researchers showed that nanofluids, particularly with carbon based materials, enhance heat transfer rate. In today era, in the case of microelectronics, small miniaturized heat sinks with high heat transfer are being developed, called micro-channel heat sinks (MCHS). The proposed work is concerned about the heat transfer behavior of aqueous suspensions of CNT nanofluids flowing through the triangular shaped microchannel. Significant enhancement of the convective heat transfer is observed and the enhancement depends on the flow conditions i.e. nusselt number, microchannel channel length, nanoparticles concentration. Particle re-arrangement, shear induced thermal conduction enhancement, reduction of thermal boundary layer due to the presence of nanoparticles, as well as the very high aspect ratio of CNT nanofluids are proposed to be possible mechanisms. Results show that thermal boundary layers distorted due to use of carbon based nanofluids and heat transfer coefficient increases about three times as compared to water.