Here,　the　mechanism　of　encapsulated　anammox　bacteria　(AnAOB)　driving　efficient　nitrogen　removal　in　the　mainstream　partial　nitritation/anammox　process　is　revealed.　The　results　show　that　a　high　nitrogen　removal　rate　(1.21±0.02　kgN·(m3·d)−1)　was　achieved　due　to　the　abundant　micropore　structure　inside　the　anammox　immobilized　filler,　ensuring　good　connectivity,　and　a　stable　aggregation　capacity,　reducing　dependence　on　extracellular　polymeric　substances.　AnAOB　were　uniformly　distributed　throughout　all　regions　of　the　immobilized　filler,　and　their　abundance　was　higher　than　that　of　the　control　anammox　granular　sludge　(AnGS).　Conversely,　cracks　appeared　on　the　surface　of　the　AnGS,　and　hollows　formed　inside.　The　metagenome　analysis　revealed　that　the　immobilized　filler　supported　the　coexistence　of　multiple　AnAOB,　and　the　appropriate　niche　enhanced　coordination　between　the　AnAOB　and　dominant　companion　microorganisms.　In　contrast,　AnGS　exhibited　stronger　NH4　+–N　and　NO2　−–N　loops,　potentially　reducing　the　total　nitrogen　removal　efficiency.　This　study　promotes　the　mainstream　application　of　anammox.　©　2024　Elsevier　Ltd