The performance degradation issue caused by carbon deposition has limited the commercial application of natural-gas-fueled solid oxide fuel cells. Most previous corresponding studies are based on thermodynamic equilibrium analyses, while long-term transient evaluation work is lacking. Therefore, a transient multi-physics numerical model is developed in present work. The corresponding long-term performance degradation evaluation is then conducted. The results show that, for a direct internal reforming solid oxide fuel cell, the increase in carbon deposition and deterioration of performance degradation were concentrated in the first 180 days of steady−state operation and slowed down at the later stage. The electrode inlet rapidly developed a high concentration of carbon deposition after 180 days of steady−state operation. The deposited carbon deteriorated the gas transport and decayed reaction activity within the porous electrode, eventually inducing a deactivation zone with 0 current density at the inlet. Key measures to inhibit carbon deposition should be implemented within the first 180 days of operation, and the pre-reformed operation of natural gas is encouraged for natural-gas-fueled solid oxide fuel cells.