Cereal/cereal and cereal/legume intercropping systems are popular in the northwest of China and often result in yield increases compared to sole cropping. The aim of this study was to investigate crop yield and the effects of intercropping on bacterial community composition in rhizosphere of wheat, maize and faba bean at different growth stages. Rhizosphere bacterial community composition was studied by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. The results showed that intercropping increased crop yield，enhanced bacterial diversity and changed bacterial community composition in rhizosphere compared to sole cropping, and the effect was most pronounced in the wheat/faba bean intercropping system when the two species at anthesis. In maize/faba bean intercropping system, the effect was only on maize in seedling. The effect was less pronounced in wheat/maize intercropping. The effects of intercropping on diversity of microbial community in the rhizosphere that may, in part, explain the yield increase compared to sole cropping. Furthermore the results provide evidence that aboveground plant diversity and belowground biodiversity are linked.