This paper is directed at the numerical simulation of pressure-driven nitrogen slip flow in long microchannels, focusing on conjugate heat transfer under uniform heat flux wall boundary condition. This problem has not been studied in detail despite its importance in many practical circumstances such as those related to the cooling of electronic devices and localized heat input in materials processing systems. For the gas phase, the two-dimensional momentum and energy equations are solved, considering variable properties, rarefaction, which involves velocity slip, thermal creep and temperature jump, compressibility, and viscous dissipation. For the solid, the energy equation is solved with variable properties. Four different substrate materials are studied, including commercial bronze, silicon nitride, pyroceram, and fused silica. The effects of substrate axial conduction, material thermal conductivity and substrate thickness are investigated in detail. It is found that substrate axial conduction leads to a flatter bulk temperature profile along the channel, lower maximum temperature, and lower Nusselt number. The effect of substrate thickness on the conjugate heat transfer is very similar to that of the substrate thermal conductivity. That is, in terms of axial thermal resistance, the increase in substrate thickness has the same impact as that caused by an increase in its thermal conductivity. By comparing the results from constant and variable property models, it is found that the effects of variation in substrate material properties are negligible.