Fusarium wilt in faba bean (Vicia faba L.) is caused by Fusarium oxysporum f. sp. fabae (FOF), which reduces the yield of crop. We used greenhouse, field and laboratory experiments to evaluate the role of organic acids in the occurrence of Fusarium wilt of faba bean to confirm the mechanism of rational application of nitrogen (N) and intercropping to alleviate Fusarium wilt. We investigated the response of organic acids exuded from the roots of faba bean to different N levels and cropping patterns (monocropping and intercropping with wheat). The results showed that the application of N and intercropping with wheat could control the Fusarium wilt of faba bean, which was closely related to the components and quantity of organic acids exuded from its roots. Among them, tartaric acid and malic acid are the most abundant and important, because they have a significant inhibitory effect on the growth and reproduction of FOF and substantially aid in the control of Fusarium wilt. The application of 90 kg ha-1 of N combined with wheat intercropping significantly controlled the Fusarium wilt and increased the grain yield of faba bean. Our results suggest that 90 kg ha-1 of N combined with intercropping is the most effective way to control Fusarium wilt and should be incorporated into agricultural management practices.