[Objective] Rhizosphere microorganisms play an essential role in the process of nutrients absorbing in crops. To improve nitrogen utilization efficiency in wheat production, it is of great significance to study effects of nitrogen deficiency on structure of the microbial community in the rhizosphere of wheat.[Method] Soil samples were collected from a nitrogen-depleted wheat field of Lou soil, which is typical of the Guanzhong Region, Shaanxi Province for a rhizobox experiment. The experiment was designed to have two treatments, one applied with nitrogen fertilizer at a normal rate (150 mg·kg^-1) and the other with no nitrogen fertilizer to the wheat growing in the rhizoboxes. Soil microbial communities in the rhizosphere, near-rhizosphere and non-rhizosphere were analyzed with the technique of 16S rRNA gene amplicon high-throughput sequencing for comparison between the two treatments in soil microbial diversity and community structure in these sections of the rhizoboxes.[Result] Results show that the content of soluble inorganic nitrogen in the soil played a leading role in triggering changes in microbial community diversity and community structure. Compared with normal nitrogen supply, soil microbial community has higher α diversity index under nitrogen deficiency. The abundance of microorganisms, such as Firmicutes, Gracilibacteria, Candidatus Jorgensenbacteria and Elusimicrobia, was negatively related to soil nitrate content. Nitrososphaeria an ammonia-oxidizing class of archaea, was a critical node of the microbial co-occurrence network affected by nitrogen deficiency. Nitrogen deficiency induced a series of microbial metabolic processes, such as mRNA synthesis, glycolysis, peroxides, and phosphoinositol metabolism. Nitrosospira and Nitrospirae contributed the most to accuracy of the random forest classifier, and can be used as biomarker for prediction of nitrogen supply level in soil.[Conclusion] To sum up, the effects of nitrogen deficiency on diversity, community structure, and metabolic function of the soil microbes in the rhizosphere were significant, and more than the rhizosphere effect. It is helpful for the exploration of plant growth-promoting rhizobacteria and provides some theoretical basis for reducing the nitrogen fertilizer application and improving the utilization efficiency of nitrogen fertilizer in wheat production.