The internal reforming and electrochemical reactions appear in the porous anode layer, and may lead to inhomogeneous temperature and gas species distributions according to the reaction kinetics. In this study, a fully three-dimensional calculation method has been further developed to simulate and analyze chemically reacting transport processes in a thick anode duct. The composite duct investigated consists of a porous anode, the fuel flow duct and solid current connector. Momentum and heat transport together with gas species equations have been solved by coupled source terms and variable thermophysical/transport properties of the fuel gas mixture. Furthermore, the heat transfer due to the fuel gas diffusion is implemented into the energy balance based on multicomponent diffusion models. The fuel cell conditions such as the combined thermal boundary conditions on solid walls, mass balances (generation and consumption) associated with the various reactions, and gas permeation between the porous anode and flow duct are applied in the analysis. Simulation results show that the internal reforming and the electrochemical reactions, and cell operating conditions are significant for species distribution, fuel gas transport and heat transfer in the subdomains of the anode.