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Fertilization is an important practical measure in agricultural production. As an important nutrient element of plants, nitrogen (N) has a significant impact on the plant productivity and microbial function. Rhizosphere microorganisms affect plant growth and development, nitrogen uptake and utilization, and ecological adaptability. The interaction mechanism between plant and rhizosphere microorganisms is one of the hotspots in life science research and the key program of agricultural microorganism utilization. In this article, the relationship among plant root morphology and physiology, rhizosphere microorganisms, and nitrogen is reviewed, summarized, and prospected.