A hard carbon build-up layer often forms on the flue wall surface in anode baking furnaces. The layer accumulates over thermal circles and needs to be mechanically removed regularly to ensure sufficient space for the anodes between flue walls. The underlying mechanisms are still unknown and the extent of the carbon build-up varies from plant to plant. The build-up on the flue wall, taken from an autopsy of an open top furnace, has been examined. Microstructure and phase compositions of the carbon build-up, especially towards the refractory interface, were studied by optical microscopy, X-ray computed tomography (CT), SEM/EDS, and XRD. Pyrolytic carbon was found to be the main part of the carbon build-up layer in addition to packing coke particles. The transport of silicon from the refractory material, condensating on the flue wall surface, is found as nucleation sites for the formation of carbon build-up. Formation mechanisms of the carbon build-up are proposed with reaction schemes supported by thermodynamic calculations.