Integrated gasification fuel cell system is one of the important candidates for the next generation clean and high efficiency power generation technology. In order to avoid carbon deposition caused by the carbon monoxide disproportionation reaction of the coal syngas in the solid oxide fuel cell stack, it is necessary to humidify the syngas to a certain extent. A multi-physics multi-scale model of the solid oxide fuel cell stack was constructed based on alternative mapping method to analyze the performance of the stack under different humidification levels. After humidification, the water gas shift reaction rate in the stack increases significantly and interacts with the electrochemical reactions of hydrogen and carbon monoxide. The water gas shift reaction is relatively strong near the inlet of the cell flow channel in the stack, rapidly converting CO to H2, and, supplementing the consumption of hydrogen in its electrochemical reaction. However, the increase of humidification degree will also reduce the Nernst potential of hydrogen and inhibit the electrochemical reaction rate of hydrogen near the inlet section of the flow channel. The partial pressures of carbon monoxide and hydrogen are close to equilibrium at a distance greater than 60 mm from the inlet of the flow passage, the water gas shift reaction is weakened, and the gas reaction rate is controlled by the electrochemical reaction. The H/O and C/O volume fraction ratio in the inlet section of the flow channel are both low, which is easy to occur carbon deposition. More than 50% humidification can significantly reduce the risk of carbon deposition in the stack. Humidification will also cause performance degradation of the stack. Under the conditions of syngas composition adopted in this paper, humidification of 100% will cause 4.65% performance degradation.