Fusarium oxysporum f. sp. fabae is the causal agent of fusarium wilt. Fusaric acid (FA), produced by F. oxysporum, plays an important role in the occurrence of disease, and intercropping is an effective measure for control of disease and for improving host resistance in plants. The objective of this study was to investigate the physiological and biochemical responses, and mechanisms of tissue structure resistance, of intercropped faba beans following exposure to different concentrations of FA. Results demonstrated that intercropping reduced the occurrence of fusarium wilt, and improved faba bean growth and yield. In addition, wheat intercropping significantly reduced red ink absorption of faba bean (33.2%), increased water content (3.1%), and increased activity of the root antioxidant enzymes peroxidase (POD) and catalase (CAT) (26.3% and 2.2.%, respectively). Furthermore, increased lignin content and callose deposition in plant vessels were observed (12.5% and 42.7%, respectively) when subjected to the highest concentration of FA stress (200 mg/L). Intercropping resulted in more intact root cell morphology, increased occurrence of intracellular vacuoles, increased cell wall thickness, and an increase in the number of mitochondria and rough endoplasmic reticulum. Intercropping alleviated the wilting effect of FA on faba bean via enhanced physiological, biochemical, and tissue structure resistance of faba bean root.