Continuous　flow　reactors　with　time　intermittent　operational　(TIO)　mode　and　spatial　intermittent　operational　(SIO)　mode　were　operated　to　evaluate　the　effects　of　operational　modes　on　the　removal　performances,　the　characteristics　of　granules　and　the　dynamics　of　microbial　communities　in　simultaneous　nitrification,　denitrification　and　phosphorus　removal　(SNDPR)　granular　system.　The　results　showed　that　the　removal　efficiency　of　TP,　TN　were　81.3%,　86.7%　under　TIO　mode,　and　70.6%,　77.4%　under　SIO　mode,　respectively.　Meanwhile,　the　PN　and　value　of　PN/PS　in　SIO　were　higher　than　those　in　TIO.　Besides,　results　of　high-throughput　pyrosequencing　illustrated　that　the　combination　of　filamentous　archaea　(Methanothrix)　and　filamentous　bacteria　(Thiothrix)　had　resulted　in　the　increase　of　EPS　and　SVI　under　SIO　mode.　Finally,　functional　bacterial　and　archaeal　species,　involving　HMA,　AMA,　AOA,　DPAOs　etc.,　were　identified　to　reveal　the　effects　of　operational　modes　on　the　mechanism　of　nutrients　removal　in　granular　SNDPR　continuous-flow　system.