Numerical study has been carried out on the laminar forced convection flow of nanofluids in a wide rectangular microchannel. The flow and heat transfer characteristics of gold and of single-walled carbon (SWCNT) nanofluids are investigated in order to find an efficient and cost-effective heat transfer fluid. The effects of nanoparticle volume concentration and of spherical and cylindrical particulate sizes on the conjugate heat transfer performance of the microchannel are reported. The effective thermal conductivity of a nanofluid is evaluated on the basis of particle sphericity by considering the volume and surface area of the nanoparticles. The average convective heat transfer coefficient increases with increase in Reynolds number and volume concentration. Moreover, sphericity-based thermal conductivity evaluation showed that increasing the length of the SWCNT nanoparticle has significant effect on the heat transfer performance, concluding that axial heat conduction dominates the radial heat conduction within the nanoparticle. The carbon nanofluid is identified as an optimized heat transfer fluid with better heat transfer characteristics in comparison with the gold nanofluid. It also reduces the cost of the working fluid. The variations in the interface temperature between solid and fluid regions are reported for nanofluids with different concentrations at different Reynolds numbers. The diameter and length of the SWCNT nanoparticle show a significant effect on heat transfer characteristics.