Abstract: Anammox is an energy-saving bioprocess for nitrogen removal with significant application potential in nitrogen-laden wastewater treatment. However, the widespread presence of recalcitrant fulvic acid (FA) in sewage jeopardizes anammox system stability, and the underlying mechanisms remain poorly understood. In this study, a lab-scale up flow anaerobic bioreactor was constructed to systematically investigate the structural transformation of FA and the associated microbial mechanisms in anammox systems. Results revealed that: (1) Significant FA structural changes occurred at low concentrations (25.3-65.1 mg/L), reduced FA aromaticity and humification of FA were observed, accompanied by sustained anammox bacterial activity (Candidatus Brocadia/Jettenia) and total nitrogen removal efficiency >80%. In contrast, high FA concentrations (>65.1 mg/L) inhibited nitrogen/FA conversion and reduced anammox bacterial relative abundance by approximately 40%. (2) Metagenomics further elucidated microbial synergy: Anaerolineaceae degraded FA macromolecules into smaller substrates, fueling partner bacteria (Denitratisoma) and mitigating FA′s inhibitory effects on anammox. (3) Gene profiling indicated FA upregulation initially suppressed nitrogen-cycle genes (delaying hydrazine utilization), and subsequently disrupted heterotrophic aromatic degradation (benzoyl-CoA→3-hydroxyadipyl-CoA pathway), compromising high-FA clearance. Research reveals that the microbial community′s catabolic prowess determines the stability of the anammox process: low concentrations of FA can be effectively decomposed by accompanying bacteria, whereas high concentrations simultaneously inhibit both nitrogen transformation and organic degradation pathways, ultimately causing systemic collapse.