A hybrid solver dynamically coupling kinetic solutions computed in local rarefied areas and Navier-Stokes solutions in the rest of the flow is used for the analysis of heat transfer in a rough microchannel. Roughness geometry is modeled as a series of triangular obstructions and a relative roughness up to 5% of the channel height is considered. Wide range of the Knudsen numbers (from 0.01 up to 0.1) is considered, at low Mach number (nearly incompressible flow). The competition between roughness, rarefaction and heat transfer effects is discussed in terms of averaged Nusselt and Poiseuille numbers and mass flow rate. Discrepancy between the full Navier-Stokes and hybrid solutions is investigated, assessing the range of applicability of the first order slip boundary condition for rough geometries with and without heat transfer.