The composite electrode structure plays an important role in the optimization of performance of the intermediate-temperature solid oxide electrolysis cell (IT-SOEC). However, the structural influence of the composite electrode on the performance of IT-SOEC is not clear. In this study, we developed a three-dimensional macroscale model coupled with the mesoscale model based on percolation theory. We describe the electrode structure on a mesoscopic scale, looking at the electrochemical reactions, flow, and mass transport inside an IT-SOEC unit with a composite electrode. The accuracy of this multi-scale model was verified by two groups of experimental data. We investigated the effects of operating pressure, volume fraction of the electrode phase, and particle diameter in the composite electrode on electrolysis reaction rate, overpotential, convection/diffusion flux, and hydrogen mole fraction. The results showed that the variation in the volume fraction of the electrode phase had opposite effects on the electrochemical reaction rate and multi-component diffusion inside the composite electrode. Meanwhile, an optimal range of 0.8−1 for the particle diameter ratio was favorable for hydrogen production. The analysis of IT-SOEC with composite electrodes using this multi-scale model enables the subsequent optimization of cell performance and composite electrode structure.