In　this　study,　a　continuous　flow　reactor　with　simultaneous　nitrification,　denitrification　and　phosphorus　removal　(SNDPR)　granular　sludge　was　operated　in　the　continuous　aeration　(CA)　and　intermittent　aeration　(IA)　modes　to　examine　the　effect　of　aeration　on　the　performance　of　continuous-flow　system.　Then　the　experimental　results　showed　that　the　IA(1)　mode　(4　h　aeration　and　1　h　non-aeration)　could　improve　the　simultaneous　nitrogen　and　phosphorus　removal　and　the　settleability　of　granules　in　continuous　flow　system.　Results　of　high-throughput　pyrosequencing　illustrated　that　the　methanogens,　AOA,　ANAMMOX,　DNB,　denitrifying　polyphosphate-accumulating　organisms　(DPAOs)　were　the　important　participant　of　simultaneous　biological　nutrients　removal　(SBNR),　meanwhile,　the　IA(1)　mode　could　effectively　inhibit　the　growth　of　filamentous　microorganisms　(Thiothrix　and　Acinetobacter).　Finally,　a　conceptual　model　of　the　SNDPR　granular　microbial　ecosystem　under　IA(1)　mode　was　proposed　as　a　base　for　analyzing　the　mechanism　of　simultaneous　nutrient　removal　in　continuous　flow　system.