Abstract Effect of utilizing porous substrates on thermal and hydraulic performance of double-layered microchannel heat sinks (MCHSs) is comprehensively analyzed in this work. Thermal resistance and pumping power of the porous double layer MCHSs are evaluated to find optimized designs which improve heat transfer while requiring lower pumping power compared to conventional MCHSs. Conjugate heat transfer is numerically simulated by developing three dimensional models of porous MCHSs with different solid and porous fin thicknesses at the top and bottom channels. For design optimization, various performance parameters are evaluated and compared to conventional microchannels by changing the porous substrate and solid fin thickness. The results show that for every combination set of geometrical parameters in double-layered MCHS, an optimized porous double-layered MCHS can be found which can enhance thermal and hydraulic performance. Studying the heat transfer effectiveness and pumping power effectiveness of the new porous double-layered MCHSs simultaneously indicate this. The enhancement is shown in all scenarios where the top and bottom channel can have different solid-porous thickness. The superior performance of porous double-layered microchannels is verified for different range of Reynolds number, porosity of substrates, and heat sink material.