The　recently　developed　Partial　Denitrification/Anammox　(PD/A)　is　an　emerging　process　for　simultaneous　ammonium　and　nitrate　removal,　while　the　remaining　organics　from　PD　may　pose　an　adverse　effect　on　the　subsequent　anammox　process.　In　this　study,　a　granule-based　anammox　UASB　reactor　was　developed　with　receiving　municipal　wastewater　driven　PD　effluent　that　contained　a　certain　amount　of　refractory　organic　matter,　the　characterization　of　different　size-fractionated　granules　on　nitrogen　removal　and　microbiological　mechanisms　were　investigated.　Anammox　activity　increased　with　granule　size,　while　an　oversize　exceeding　2.5　mm　would　lead　to　activity　reduction.　Significant　denitrification　activity　was　detected,　it　exhibited　a　contrary　relationship　with　anammox　activity.　Delightedly,　the　denitrification　was　observed　to　proceed　with　high　nitrite　accumulation,　especially　in　smaller　granules　with　nitrate-to-nitrite　transformation　ratio　(NTR)　above　84.4%.　These　results　were　confirmed　by　microbial　analysis,　anammox　genus　including　Candidatus　Kuenenia,　Brocadia,　and　Jettenia　were　identified　in　all　granules,　their　abundances　increased　with　granule　size,　and　the　dominated　Kuenenia　preferred　to　grow　in　larger　granule.　Various　kinds　of　denitrification　bacteria　were　detected　with　the　relative　abundances　increased　with　the　decrease　in　granules　size.　Particularly,　the　Thauera　that　responsible　for　PD　with　high　nitrite　accumulation　was　revealed　to　grow　in　such　system,　its　relative　abundance　in　small-size　granules　(12.9%,　＜0.5　mm)　was　much　higher　than　the　large　ones　(＜2.3%).　Overall,　this　study　improved　our　understanding　of　the　synergy　of　anammox　and　denitrification　bacteria　between　size-fractionated　granules,　it　provides　a　guide　for　system　optimization　towards　great　stability　by　biomass　segregation　strategy,　and　sheds　new　light　to　develop　an　efficient　anammox　coupling　with　PD　process　in　continuous-flow　UASB　reactor.