Convective heat transfer in a channel partially filled with porous medium has received a lot of attention due to its wide engineering applications. However, most researches focused on a channel partially filled with single layer porous medium. In this paper, we will analyze the heat transfer and entropy generation inside a channel partially filled with N-layer porous media. The flow and the heat transfer in the porous region are described by the Darcy–Brinkman model and the local thermal nonequilibrium model, respectively. At the porous-free fluid interface, the momentum and the heat transfer are described by the stress jump boundary condition and the heat flux jump boundary condition, respectively; while at the interface between two different porous layers, the momentum and the heat transfer are described by the stress continuity boundary condition and the heat flux continuity boundary condition, respectively. The analytical solutions for the velocity and temperature in the channel are derived and used to calculate the overall Nusselt number, the total entropy generation rate, the Bejan number, and the friction factor. Furthermore, the performances of the flow and heat transfer of a channel partially filled with third-layer porous media are studied.