Abstract: Understanding how irrigation and fertilization strategies modulate root-soil interactions is critical for optimizing crop productivity and soil health in greenhouse systems. Root exudates act as key mediators in rhizosphere biochemical processes, yet their response to variations in aerated irrigation and nitrogen levels remains insufficiently explored. To address this knowledge gap, this study employed non-targeted metabolomics to investigate how aerated drip irrigation and nitrogen application level affect the composition and metabolic pathways of root exudates in greenhouse-grown pepper (Capsicum annuum L.). This approach was selected for its high sensitivity and ability to comprehensively profile complex exudate mixtures, providing detailed insight into plant metabolic responses. A randomized block experiment was conducted with three nitrogen levels (zero level 0 kg/hm², low level 140 kg/hm², and conventional level 210 kg/hm²) and two irrigation methods (conventional drip irrigation: air void fraction 0%; aerated drip irrigation: air void fraction 15%). Results showed that compared with conventional drip irrigation, aerated drip irrigation significantly increased soil oxygen diffusion rate (ODR), oxidation-reduction potential (ORP) and soil respiration rate by 10.9%, 14.83%, and 21.84%, respectively (P<0.05). In addition, aerated drip irrigation changed the soil nitrogen conversion process, and the nitrate nitrogen content by 13.11% (P<0.05) and unease activity by 9.68% (P<0.05), while reducing ammonium nitrogen and alkali-hydrolyzable nitrogen by 7.05% and 12.29%, respectively (P<0.05). These metabolite changes indicate synergistic effects of irrigation oxygenation and nitrogen availability on root metabolic outputs. Liquid chromatography-mass spectrometry (LC-MS) identified 321 compounds in positive ion mode and 167 in negative ion mode, mainly including lipids, lipid-like molecules, organic acids, and their derivatives. Compared with conventional drip irrigation, 38, 49 and 45 significantly different metabolites were screened out by aerated drip irrigation, including 17, 26 and 29 metabolites with no nitrogen application, low nitrogen and conventional nitrogen, respectively, and 21, 23 and 16 down-regulated metabolites. The discovery of these differential metabolites provides a key clue for further exploring the regulatory effect of aerated drip irrigation and nitrogen fertilization on root exudate metabolism in pepper. KEGG pathway analysis revealed significant enrichment in glycine, serine, and threonine metabolism, as well as in ABC transporter pathways. Redundancy analysis showed that soil environmental factors explained 43.36% of the variation in root exudate profiles, with ODR, ORP, and nitrate nitrogen identified as key drivers. This study demonstrates that aerated drip irrigation plays a crucial role in influencing the metabolism of root exudates in peppers by regulating the soil environment. This finding not only enriches our understanding of the mechanisms by which aerated drip irrigation and nitrogen application interact in the cultivation of peppers, but also provides important theoretical support and practical evidence for the development of a highly efficient cultivation model for peppers based on metabolic regulation.