Aims <p>Invasion by Solanum rostratum Dunal destabilizes ecosystems; however, the changes it induces in the rhizosphere soil microenvironment remain poorly understood. This study aimed to investigate how microbial diversity and metabolite profiles in rhizosphere soil respond to S. rostratum invasion.</p> Methods <p>We conducted a comparative study of rhizosphere and bulk soils from two sites with varying invasion densities: Changzi village and Weizi village. Microbial diversity was assessed using sequencing techniques, and metabolite profiles were analyzed using advanced metabolomics methods. Soil physicochemical parameters were also measured to explore correlations.</p> Results <p>In Changzi village, bacterial diversity in rhizosphere soil significantly decreased compared to bulk soil. Dominant taxa included Acidobacteria (bacteria) and Ascomycota (fungi). Soil properties showed notable variation: in Weizi village, microbial communities were significantly correlated with organic nitrogen, while in Changzi village, correlations were stronger with total nitrogen. The invasion also altered metabolite profiles, affecting classes such as phospholipids, organonitrogen compounds, and fatty acids. Metabolic pathways like amino sugar and nucleotide sugar metabolism were significantly impacted.</p> Conclusions <p>The study demonstrates that S. rostratum invasion significantly alters the microbial community structure, metabolite composition, and soil physicochemical parameters in rhizosphere soil. These changes suggest a complex, interlinked response that ultimately contributes to ecosystem destabilization.</p>