Abstract: To address the low and unstable nitrogen-phosphorus removal efficiency of conventional bioretention systems, this study develops an iron-carbon modified bioretention facility (IC-B) and investigates its synergistic nutrient removal mechanisms under simulated rainfall intensities (7, 17, 21 mm/h), pre-rain drought periods (1, 3, 10 days), and inundation zone heights (0, 400 mm). The experimental setup comprises acrylic columns filled with iron-carbon media (1:1 mass ratio), alongside biochar (BC-B) and traditional sand (TR-B) control groups. Water quality parameters (nitrate, ammonium, total nitrogen, and total phosphorus) are analyzed via UV spectrophotometry, while microbial communities and reaction pathways are evaluated through high-throughput sequencing and substrate nitrification/denitrification potential tests. Results demonstrate that IC-B achieves average nitrate nitrogen and total phosphorus removal rates of 94.17% and 97.57%, representing 46.2% and 33.4% improvements over TR-B, respectively. The iron-carbon media enable multi-path coupling: biochar establishes adsorption barriers in the vadose zone, while iron fillings accelerate oxygen depletion, synergistically creating anoxic microenvironments that enrich denitrifying bacteria (Proteobacteria abundance: 38.57%). Fe³⁺/Fe²⁺ redox cycling mediated by Acidobacteriota enhances system stability, simultaneously promoting chemical phosphorus precipitation and biological denitrification. A 400-mm inundation zone height significantly improves denitrification efficiency, whereas extended drought periods (10 days) do not trigger phosphorus leaching. This study elucidates the synergistic mechanisms of iron-carbon modified bioretention systems, offering technical insights for urban non-point source pollution mitigation.