<p>Anaerobic ammonium oxidation (anammox) is an efficient, low-consumption biological nitrogen removal technology, and it shows great potential in wastewater treatment. However, the activity of anammox bacteria is inhibited by high concentrations of key substrates, including ammonia (NH₄⁺), nitrite (NO₂⁻), and organic compounds (such as antibiotics, metals, and other toxicants), through multiple mechanisms. This inhibition has restricted the full-scale engineering application of anammox. Existing literature mainly focuses on single-factor inhibition mechanisms. Moreover, mitigation strategies validated in laboratories have limited effectiveness in complex substrate environments. To fill the above gaps, this review constructs a three-dimensional analytical framework that integrates the fundamental mechanisms, hierarchical mitigation strategy design, and dynamic application verification. It systematically clarifies the synergistic inhibition pathways of ammonia, nitrite, and organic matter. Notably, it emphasizes revealing the multilevel inhibitory mechanisms of organic matter on anammox bacteria. Furthermore, the research proposes a tiered mitigation strategy that integrates microenvironment regulation, microbial community enhancement, and process integration. It also summarizes relevant kinetic models, which can support the prediction, analysis, and engineering optimization of inhibition effects in anammox systems. These findings provide fundamental insights into the concentration threshold effects of substrate inhibition and the molecular interference mechanisms of organic matter. Thus, they offer effective methodologies to enhance the operational stability and application efficiency of anammox technology.</p>