It is of great significance to explore the differences of nitrogen-fixing microbial communities and metabolism in the rhizosphere of soybean under different nitrogen applications for reasonable and effective regulation of rhizosphere ecosystems and improvement of soil nutrient use efficiency. Soil metabolomics and high-throughput sequencing techniques were used to study the effects of different nitrogen applications on soil metabolites and nitrogen-fixing microbial community structure in soybean rhizosphere. The results showed that there were significant differences in community structure and soil metabolites of nitrogen-fixing bacteria in soybean rhizosphere soil under no nitrogen treatment and nitrogen treatment. A total of 29 differential metabolites were detected in the experiment, including organic acids, polyketides, fatty acyl compounds, organic nitrogen-containing compounds and other substances. Nitrogen applications promoted the up-regulation of most metabolites. The analysis of differential metabolite pathways showed that differential metabolites were mainly enriched in amino acid synthesis and carbohydrate metabolism. In addition, the nitrogen applications changed the microbial community structure, resulting in a significant decrease in the relative abundance of Bradyrhizobium, Azohydromonas, Frankia and Sinorhizobium in the rhizosphere soil. Correlation analysis showed that inter-rhizosphere dominant nitrogen-fixing bacteria were significantly negatively correlated with most of the up-regulated differential metabolites and significantly positively correlated with the down-regulated differential metabolites. The results provided a theoretical basis for the effects of different nitrogen fertilizations on microbial communities and metabolites in soybean rhizosphere soil.