In micro heat exchangers, due to the presence of distributing and collecting manifolds as well as hundreds of parallel microchannels, a complete conjugate heat transfer analysis requires a large amount of computational power. Therefore in this study, a novel methodology is developed to model the microchannels as a porous medium where a compressible gas is used as a working fluid. With the help of such a reduced model, a detailed flow analysis through individual microchannels can be avoided by studying the device as a whole at a considerably less computational cost. A micro heat exchanger with 133 parallel microchannels (average hydraulic diameter of 200 m) in both cocurrent and counterflow configurations is investigated in the current study. Hot and cold streams are separated by a stainless-steel partition foil having a thickness of 100 μm. Microchannels have a rectangular cross section of 200 μm x 200 μm with a wall thickness of 100 μm in between. As a first step, a numerical study for conjugate heat transfer analysis of microchannels only, without distributing and collecting manifolds is performed. Mass flow inside hot and cold fluid domains is increased such that inlet Reynolds number for both domains remains within the laminar regime. ... mehrInertial and viscous coefficients extracted from this study are then utilized to model pressure and temperature trends within the porous medium model. To cater for the density dependence of inertial and viscous coefficients due to the compressible nature of gas flow in microchannels, a modified formulation of Darcy–Forschheimer law is adopted. A complete model of a double layer micro heat exchanger with collecting and distributing manifolds where microchannels are modeled as the porous medium is finally developed and used to estimate the overall heat exchanger effectiveness of the investigated micro heat exchanger. A comparison of computational results using proposed hybrid methodology with previously published experimental results of the same micro heat exchanger showed that adopted methodology can predict the heat exchanger effectiveness within the experimental uncertainty for both cocurrent and counterflow configurations.