An additive manufactured triangular cross section microchannel heat sink (MCHS) is experimentally investigated by comparing parallel and counter flow arrangement. It consists of dual microchannel with hydraulic diameter of 650 µm, where the emphasize is given on the influence of flow configuration and rough wall structure on thermal performance of MCHS. Pressure drop, Nusselt number, thermal resistances, thermal performance index and temperature gradient across microchannel are evaluated and compared. For flow rate between 1 ml/min - 5 ml/min, counter flow offers more uniform temperature distribution across MCHS surface at a maximum difference of 37.2% and generates lower pressure drop by at least 25 % compared to parallel flow configuration. As Reynold number exceeds 140, parallel flow Nusselt number is greater which leads to superior thermal performance index (TPI) between 12.7 % - 25.9 %. Convective thermal resistance is found to be the dominant thermal resistance compared to capacitive and conductive thermal resistance. To conclude, at flow rate below 5 ml/min, counter flow offers the best thermal performance due a more uniform thermal gradient across MCHS surface and negligible differences in TPI between both flows configuration. At a higher flow rate of 5 ml/min and above, thermal gradient is independent of flow configuration and parallel flow is preferred due to higher TPI.