Plenty of reports about effects of intercropping improving yield and reducing disease incidence are available, but little was reported about the mechanism of the effects. RAPD and T-RFLP methods were used to study effects of intercropping of cucumber with wheat, vicia villosa and clover, individually, on cucumber disease indexes, cucumber rhizosphere soil microbial community diversity and yield. Results showed that intercropping of cucumber with wheat and vicia villosa increased soil microbial community diversity in cucumber rhizosphere, and the effect of the latter was the most prominent. All intercropping modes increased cucumber yield significantly (p< 0.01), and the effect of the intercropping of cucumber with wheat was more significant over that of the others. Meanwhile, intercropping decreased disease indexes of angular leaf spot, powdery mildew, downy mildew and Fusarium wilt, and decreased population of Fusarium oxysporum no matter with what plant. So it is quite obvious that intercropping increasees soil microbial community diversity and yield of cucumber, but mitigates diseases.