Field experiment was conducted to examine the effects of wheat and faba bean intercropping on rhizosphere microbial community functional diversity and occurrence of faba bean fusarium wilt. Results showed that fusarium wilt incidence and disease index of faba bean were significantly decreased by 8.72% and 25.81% in wheat and faba bean intercropping system. Comparing with monocropping,intercropping significantly increased the average well color development(AWCD) of wheat and faba bean, and the AWCD value of intercropped faba bean was the highest and the monocropped faba bean was the lowest, AWCD value of intercropped faba bean was increased by 82.7% when compared with monocropping. Functional diversity index of Shannon index (H) and substrate richness (S) in Biolog ECO microplates were significantly higher in intercropping than in monocropping system. Substrate richness of intercropped wheat and faba bean were increased by 29.2% and 30.3% respectively. The carbon sources with higher utilization intensity percentage by rhizosphere microbes were carbohydrates, amino acids and carboxylic acids, c.e. 41.96%, 19.80% and 18.13% respectively. Principal component analyses and correlation analyses demonstrated that the significant difference between monocropping and intercropping mainly depended on amino acids-dominated carbon sources and secondarily on carbohydrates and carboxylic acids. Intercropping had improved AWCD value, Shannon-wiener diversity index and richness of wheat and faba bean, changed soil microbe community functional diversity. Therefore, intercropping could be an effective measure to control faba bean fusarium wilt occurrence. It established the theory foundation for explanations diseases control in intercropping system.