A field trial was conducted to investigate the effects of three different faba bean cultivars [92-24 (92-24), Yundou 324 (YD324), Fengdou 6 (FD6)]and wheat intercropping on yield, disease index of fusarium wilt, amount of Fusarium oxysporum on faba bean, functional diversity of the fungal community, and enzyme activities in the rhizosphere of faba bean. Results showed that in comparison with that of mono-cropping, aboveground dry weight,grain yield, and 100-seed weight of faba bean were significantly increased by use of YD324 with wheat intercropping (YD324/W), and by use of FD6 with wheat intercropping (FD6/W). The disease index of fusarium wilt, and the amount of Fusarium oxysporum on YD324 decreased significantly (57.14% and 32.06%, respectively) as did those of FD6 (41.67% and 29.88%, respectively) as they were intercropped with wheat, but use of 92-24 caused no significant change. The Shannon diversity index (H) and substrate richness (S) in Biolog FF microplates of YD324/W and FD6/W were significantly higher than those for faba bean from mono-cropping. In comparison with the values for mono-cropping, the average well color development value (AWCD) of faba beans with YD324/W and FD6/W was increased by 61.75% and 46.49%, respectively. The fungal communities of faba bean rhizosphere were also changed with YD324/W and FD6/W, but use of 92-24 with wheat intercropping (92-24/W) had no significant impact on H, S, AWCD value, and fungal community. During different stages of fusarium wilt occurrence in the faba beans, the activity of invertase, urease, and catalase in the faba bean rhizosphere increased with YD324/W and FD6/W, but not with 92-24/W. Faba bean with wheat intercropping could change fungal communities; increase fungal activity, Shannon diversity index, and substrate richness; and promote soil enzyme activities. It is suggested that wheat and faba bean intercropping plays an important role in rhizosphere soil microenvironment. This could reduce the amount of Fusarium oxysporum and control the build-up of soil-borne disease caused by continuous faba bean cultivation, but the effects of intercropping are influenced by the faba bean cultivars used.