The present study is a genuine attempt to improve the thermal behavior and hydraulic performance of a conventional microchannel heat sink (MCHS) using porous material, phase change material (PCM) and nanofluid. Three-dimensional microchannels with square, circular and flattened circular geometries are examined numerically by considering the thermal conduction in solid parts. Various factors are examined, including the effect of the number of channels, fluid velocity passing through channels, porous substrate thickness, PCM layer thickness, Darcy number, porosity coefficient, thermal conductivity ratio in the porous material, volume fraction and nanoparticle diameter. According to the findings, for a critical thickness of the porous substrate, the thermal performance is at its minimum. With increasing values of Darcy number, porosity coefficient, nanoparticle diameter and PCM thickness, the thermal performance of MCHS decreases. An MCHS with square geometry displays a better thermal performance compared to the other two geometries. Furthermore, the use of porous material, nanofluid and PCM improves the thermal behavior compared with a conventional microchannel. The thermal performance of MCHS with PCM is approximately 47% and 17% higher than that of a microchannel with the porous substrate and a microchannel incorporating a combination of the porous layer and nanofluid.