This study numerically investigates and analyse a three-dimensional geometric parameters required in the design of a microchannel heat sink (MCHS) filled with vertical and horizontal porous substrate using nanofluid as working fluid. The aim of this study is to minimize temperature of hotspots in the heat sink of the microchannel heat sink at various geometry porosity and nanofluid volume fractions using computational fluid dynamics tool. A fixed axial length of 10 mm was used for the solid substrate, with a total volume of 0.9 mm³. Al₂O₃-water and CuO-water are used as working fluid. The vertical geometric configuration resulted in the best performance with a combination of CuO-water nanofluid and porosity of 0.25 for the copper porous substrate. Also, the total entropy generated using CuO-water is observed to be lower than the total entropy generated using Al₂O₃-water for each corresponding volume fraction. The effect of nanofluid concentration and porosity on heat transfer coefficient, thermal resistance and thermal uniformity was also reported. The results obtained showed that heat transfer performance was enhanced with an increase in the volume fraction of the nanofluid, decrease in the porosity of the porous substrate and an increase in pressure drop.