【Objective】 In China, rice and wheat rotation is an important mode of agricultural production, composed of two subsystems i.e. flooded-cultivation and dry farming, with rice and wheat being the representative respectively. The two subsystems differ significantly in irrigation and fertilization condition and soil microbial community structure. The migration of soil active components and microbial characteristics as affected by rhizosphere effect are crucial to the formation and development of soil fertility. Bacterial communities play an essential role in biogeochemical cycles, plant nutrition and disease biocontrol. Most papers available in the literature focused mainly on rhizosphere effect, root exudates and enzyme activity in the upland soil, with little efforts on comparison between upland and paddy soils in pattern of rhizosphere effect and associated microbial community dynamics. Therefore, it is so far still unclear about rhizosphere effects of rice and wheat and their relative contributions to soil function. 【Method】 A pot experiment cultivating rice and wheat separately was conducted in gleyic-stagnic anthrosols, a typical type of soil in the Changshu Ecological Experiment Station of the Chinese Academy of Sciences. Rhizosphere soil was separated from non-rhizosphere or bulk soil with a rhizobox system. Comparison was made between the two portions of soil in content of soil active components, dehydrogenase activity, microbial biomass carbon and bacterial community composition under the two cropping systems for analysis of differences between rice and wheat in rhizosphere effect. Principal component analysis (PCoA) and canonical correspondence analysis (CCA) was performed of the results of High throughput sequencing of the obtained data for analysis of soil bacterial community composition.【Result】 In both rice and wheat soils, the two portions of soil varied significantly in content of dissolved organic carbon and microbial biomass carbon and in dehydrogenase activity. Obviously they were higher in the rhizosphere than in the bulk soil, whereas dissolved organic nitrogen content and bacterial alpha diversity was significantly lower in the rhizosphere than in the bulk soil. Proteobacteria and Bacteroides were the dominant bacteria in both rice and wheat soils, accounting for more than 40%. However, in terms of dominant genera, differences were obvious between rice and wheat as well as between rhizosphere and non-rhizosphere. On the whole, soil microbial community was more complex in the rhizosphere than in the non-rhizosphere soil, and higher in population in the rice soil than in the wheat soil. Principal component analysis clearly shows that sharp difference existed between the two soil systems cultivated with rice and wheat in bacterial community, and the difference between rhizosphere and non-rhizosphere soils was significantly sharper in the wheat soil than in the rice soil. Rhizosphere effects (DOC: 2.07%; MBC: 8.61%; dehydrogenase activity: 41.11%; DON: 61.07%; and Chao1: 7.62%) in the rice soil were all lower in absolute value than their respective ones in the wheat soil (DOC: 3.37%; MBC: 22.62%; dehydrogenase activity: 44.48%; DON: 71.43%; and Chao1: 16.59%). 【Conclusion】 All the above listed findings suggest that the difference between rhizosphere and non-rhizosphere was narrower in the rice soil than in the wheat soil, that is to say, the rhizosphere effect of rice is lower, facilitating transport of photosynthetic carbon and soil nutrients and favoring growth of soil microbes, especially in rhizosphere. And the findings illustrate from a new angle the rhizosphere effect and mechanism of the effect on sustainable development of the soil under the rice and wheat rotation system, and shed lights on a new perspective for improving soil fertility, especially in the soil under upland cropping systems.