In　the　presence　of　organic　matter,　the　granular　anammox　system　under　sequencing　batch　mode　showed　more　robust　anammox　performance　than　that　under　completely　mixed　mode,　which　was　attributed　to　the　better　biomass　retention　with　high　settling　ability　and　stability　of　granular　sludge.　Based　on　the　specific　anammox　activity　test,　stratified　and　mixed　distribution　of　heterotrophic　bacteria　was　found　under　completely　mixed　and　sequencing　batch　mode,　respectively.　The　stratified　microbial　distribution　resulted　in　low　enzyme　activity　of　anammox　bacteria　and　sludge　disintegration　by　hindering　substrate　transfer　with　a　large　accumulation　of　EPS　on　the　granular　surface.　Whereas　the　heterotrophic　bacteria　mixed　in　granules　(mixed　microbial　distribution)　act　as　a　＂skeleton＂,　which　increased　the　particle　size,　density,　and　stability　of　granular　sludge.　Compared　with　biokinetic-based　selection,　diffusion-based　selection　with　high　substrate　penetration　depth　more　likely　resulted　in　the　mixed　granular　structure　and　strong　resistance　to　organic　inhibition　under　sequencing　batch　mode.