In order to investigate the rhizosphere interaction mechanism of rapeseed and flue-cured tobacco and its influence on soil balance，a pot experiment was set up to make the rhizosphere of flue-cured tobacco and rapeseed fully interact during the vegetative growth stage. 16S rDNA high-throughput sequencing and liquid chromatography-mass spectrometry(LC-MS/MS)detection techniques were used. The changes of crop rhizosphere soil nutrients，enzyme activity，microbial diversity and differential metabolites after planting rapeseed，and their combined effects on regulating the utilization of soil nitrogen，phosphorus and potassium were analyzed to clarify the response mechanism of rapeseed planting to soil nutrient balance.The results showed that，compared with monoculture of tobacco，the contents of soil organic matter，hydrolyzed nitrogen and available phosphorus were increased after intercropping with rapeseed，and the soil urease activity was significantly improved. The relative abundance of Penicillium and Fusarium fungi of tobacco rhizosphere soil was increased，and the abundance of Humicola fungi was significantly reduced. The relative abundance of bacteria such as Burkholderia in rhizosphere soil of tobacco，Blastomonas，Blastomonas，and Burkholderia in rhizosphere soil of rapeseed was reduced. In addition，the content of differential metabolites in the rhizosphere soil of tobacco was reduced，and was mainly enriched in alanine，aspartic acid and glutamic acid metabolism，ABC transporter and galactose metabolism pathway，while the rhizosphere soil of rapeseed was mainly enriched in glucosinolate biosynthesis，ABC transporter and galactose metabolism pathway. In conclusion，intercropping with rapeseed affected the microbial community diversity and function，and also the metabolites in the soil，which improved the nutrients of nitrogen，phosphorus and potassium in the soil. This study provided a theoretical basis for improving tobacco-planting soil by changing planting patterns.