The　effluent　from　the　secondary　biological　treatment　of　sewage　plant　usually　has　a　low　C/N　ratio　and　low　biodegradability,　additional　carbon　sources　should　be　added　in　its　deep　denitrification　process.　To　address　this　problem　and　meet　the　sewage　recycling　technology　demand　for　the　deep　removal　of　total　nitrogen　(TN),　total　phosphorus　(TP),　and　micro-pollutants　in　the　secondary　treatment　effluent,　a　multifunctional　composite　denitrification　system　based　on　three-dimensional　biofilm　electrode　reactor　process　(3DBER)　was　developed　in　this　study　by　changing　the　composition　of　filler　materials　in　the　traditional　3DBER.　This　new　system　could　achieve　enhanced　denitrification　and　simultaneous　removal　of　phosphorus　and　micro-pollutants　(dibutyl　phthalate　(DBP)　and　o-benzene　Dicarboxylic　acid　(2-ethylhexyl)　ester　(DEHP),　which　were　represented　by　PAEs).　The　technical　approaches　of　the　multifunctional　3DBER　process　and　the　corresponding　micro-action　mechanisms　for　pollutant　removal　were　examined　from　the　perspectives　of　process　performance　and　microbial　population　distribution.　The　results　showed　that　the　sulfur/iron　composite　functional　filler　was　a　key　factor　for　achieving　deep　denitrification　and　simultaneous　removal　of　phosphorus　and　micro　pollutants　for　the　secondary　biological　treatment　effluent　with　a　low　C/N　ratio.　The　denitrification　efficiency　of　the　multifunctional　composite　system　increased　by　about　20%　compared　with　the　traditional　3DBER　process,　the　simultaneous　TP　removal　rate　reached　80%　and　the　PAEs　removal　rate　were　above　90%.　The　analysis　from　chemometrics　and　molecular　biology　technologies　showed　that　there　was　a　synergistic　promotion　effect　among　microbial　ecology,　electron　donor　compensation,　and　pH　balance　in　the　process　of　denitrification　and　phosphorus　removal.　The　function　of　nitrogen　removal　was　due　to　the　joint　action　of　heterotrophic　and　various　autotrophic　denitrification,　and　the　key　to　phosphorus　removal　was　the　continuous　corrosion　of　sponge　iron.　The　removal　of　PAEs　was　the　result　of　the　synergistic　effect　of　adsorption,　electrochemical　oxidation,　and　biodegradation.　The　results　can　provide　theoretical　and　technical　guidance　for　developing　advanced　treatment　processes　for　the　simultaneous　denitrification,　phosphorus　removal,　and　micro　pollutant　removal　from　secondary　biological　treatment　effluent.　©　2021,　Editorial　Board　of　China　Environmental　Science.　All　right　reserved.