Porous microchannel heat sinks (MCHSs) and nanofluids are promising approaches for high-density thermal management, yet their combined thermo-hydraulic performance remains insufficiently understood. This study presents a three-dimensional numerical investigation of MCHSs incorporating porous substrates, carbon nanotubes (CNT), and water nanofluids. The effects of porous layer thickness, fin thickness, nanofluid volume fraction, and inlet velocity on pressure drop, Reynolds number, and heat transfer coefficient are systematically analyzed. Results demonstrate that increasing porous thickness consistently enhances the heat transfer coefficient exponentially. However, it simultaneously increases pressure drop, with no optimal thickness identified within the studied range. Fin thickness modulates both hydrodynamics and heat transfer, with thicker fins enabling improved heat spreading and amplifying the benefits of porous coatings. Nanofluid loading increases both viscosity and effective thermal conductivity, yielding higher pumping requirements but substantial thermal enhancement. Inlet velocity further influences these trends, with the strongest sensitivity to porous thickness observed near 1.2 m/s, corresponding to a Darcy–Forchheimer crossover regime. The findings highlight the delicate balance between hydraulic penalty and thermal augmentation in porous MCHSs with nanofluids. The correlations and design insights provided here offer a valuable framework for optimizing compact cooling systems in electronics, power devices, and other high-flux applications.