The　characteristics　of　anammox　granular　sludge　(AnGS)　based　on　color　differentiation,　and　the　regulation　mechanism　of　immobilized　fillers　in　the　system　were　investigated.　The　results　showed　that　biomass　content,　EPS　and　activity　of　red　AnGS　(R1)　were　higher　than　those　of　brown　AnGS　(R2).　Moreover,　R1　showed　nitrification,　while　R2　showed　denitrification.　Filamentous　bacteria　constituted　the　granule　skeleton　of　R1,　while　R2　mainly　constituted　inorganic　nucleation　and　granulation.　Additionally,　immobilization　improved　the　contribution　rate　of　Anammox,　and　involved　different　regulatory　mechanisms.　High-throughput　sequencing　analysis　showed　that　R1　encapsulation　biomass　eliminated　miscellaneous　bacteria　and　established　specific　flora,　while　mixed　encapsulated　biomass　of　R1　and　R2　re-formed　a　functional　bacterial　network,　which　strengthened　interspecies　cooperation.　The　R2　encapsulated　biomass　and　AnAOB　copy　numbers　were　inferior　and　the　interspecific　cooperation　was　weak,　resulting　in　an　unsatisfactory　nitrogen　removal　performance.　These　results　can　strengthen　the　understanding　and　optimization　of　AnGS　and　its　immobilization　system.