Aims Compound disease, a complex of multiple diseases, represent one of the most significant biological stresses faced by agricultural systems. However, it is not known whether nitrogen (N) supply in the intercropping system can regulate the damage caused by compound disease in faba bean and reduce yield and economic loss. Methods This two-year continuous field study investigated the effects of different levels of N supply, cultivation pattern, and disease management measures on the compound disease severity, growth parameters, yield, and economic benefits of faba bean. Results N supply increased the damage caused by compound disease to monocropping faba bean (MF) and intercropping faba bean (IF) (p < 0.05). However, this damage was less than that of the sum of the two single diseases. Although N supply increased the damage caused by compound disease in faba bean, it decreased the disease control efficacy (RCE) of IF. Interestingly, in N1 treatment, the RCE of IF did not significantly decrease; however, the epidemic "peak" of compound disease has indeed decreased. Moreover, the yield loss and its ratio of IF were lower than that of MF, with a partial land equivalent ratio (pLER) > 0.33. Further, initially, intercropping displayed an increase in the total effect (TE), other effects (OE), and disease inhibition effect (DIE), but subsequently decreased with the application of N supply. These data indicated that N1 treatment resulted in maximal effects and economic benefits. Conclusions The combination of intercropping with an adequate N supply proves effective in reducing the damage caused by compound disease, minimizing yield loss in faba bean, increasing the DIE, and maximizing the potential yield benefits of intercropping.