Soilborne Fusarium wilt is a key factor restricting the cultivation of faba bean. Intercropping faba bean and wheat effectively alleviate faba bean Fusarium wilt. This study analyzed the mechanism by which cinnamic acid promotes Fusarium wilt and the mechanism that enables intercropping alleviated Fusarium wilt. Faba beans were inoculated with Fusarium oxysporum f. sp. fabae (FOF), while the controls were not inoculated. Different concentrations of cinnamic acid were added to the inoculated plants to study the occurrence of Fusarium wilt, seedling growth, the activities of cell wall degradation enzyme (CWDESs) produced by FOF in the root, defense enzymes, total phenolics and lignin, levels of expression of the pathogenesis-related genes (PRs) PR1, PR2, and PR10, and changes in the submicroscopic cell wall structure of the roots under monocropping and intercropping systems. Cinnamic acid increased the activities of CWDEs produced by FOF in the roots, increased the activities of phenylalanine ammonia lyase and polyphenol oxidase and the contents of total phenolics and lignin, and upregulated the levels of expression of PRs in the root, but it decreased the activity of peroxidase. Transmission electron microscopy (TEM) observations identified severe damage and disruption of the root cell walls, and numerous FOF mycelia entered the cytoplasm from the cell wall. The combination of these factors increased the occurrence of Fusarium wilt. The activities of CWDEs produced by FOF in the roots decreased by intercropping wheat with faba bean, which increased the resistance of the root cell walls to infection and decreased the Fusarium wilt.