Abstract: Irrigation and fertilization can be widely used to modulate the root-soil interactions in sustainable agriculture. It is also critical to optimize crop productivity and soil health in greenhouse systems. Root exudates can act as the key mediators in rhizosphere biochemical processes. Yet it is often required for their response to the variations in the aerated irrigation and nitrogen levels. In this study, the non-targeted metabolomics was employed to investigate the effects of the aerated drip irrigation and nitrogen application level on the composition and metabolic pathways of the root exudates in greenhouse-grown pepper (Capsicum annuum L.). The high sensitivity to profile complex exudate mixture was selected to provide some insight into the plant metabolic responses. A randomized block experiment was conducted with three nitrogen levels (zero level 0, low level 140 kg/hm², and conventional level 210 kg/hm²) and two irrigation modes (conventional drip irrigation: air void fraction 0; and aerated drip irrigation: Air void fraction 15%). Results showed that the aerated drip irrigation significantly increased the soil oxygen diffusion rate (ODR) and oxidation-reduction potential (ORP) by 10.90% and 14.83%, respectively (P<0.05), compared with the conventional drip irrigation. In addition, aerated drip irrigation significantly altered soil nitrogen transformation. Compared to conventional drip irrigation, aerated drip irrigation significantly increased the nitrate nitrogen content by 13.11% (P<0.05) and unease activity by 9.68% (P<0.05), while reducing ammonium nitrogen by 7.05% on average (P<0.05). These changes indicate synergistic effects of irrigation-induced oxygenation and nitrogen availability on root-associated metabolic outputs. Liquid chromatography-mass spectrometry (LC-MS) was used to identify 321 compounds in the positive ion mode, and 167 in the negative ion mode, mainly including the lipids, lipid-like molecules, organic acids, and their derivatives. Compared with conventional drip irrigation, 38, 49 and 45 significantly different metabolites were identified under aerated drip irrigation at zero, low, and conventional nitrogen levels, respectively, including 17, 26 and 29 up-regulated metabolites, and 21, 23 and 16 metabolites were down-regulated. The identification of these differential metabolites provides important insights into the regulatory effects of aerated drip irrigation and nitrogen fertilization on root exudate metabolism in pepper. KEGG pathway analysis revealed that there was a significant enrichment in the glycine, serine, and threonine metabolism, as well as in ABC transporter pathways. Redundancy analysis showed that the soil environmental factors explained 43.36% of the variation in the root exudate profiles, where the ODR, ORP, and nitrate nitrogen were identified as the key drivers. The aerated drip irrigation can play a crucial role in the metabolism of the root exudates in peppers under the soil environment. This finding can be expected to regulate the aerated drip irrigation and nitrogen application in the cultivation of the peppers. Important theoretical support and practical evidence can also be offered for a highly efficient cultivation model for peppers using metabolic regulation.