Anaerobic　ammonium　oxidation　(anammox)　has　been　successfully　applied　to　the　practical　wastewater　treatment　due　to　a　high　nitrogen　removal　performance,　low　sludge　yield　and　low　operating　cost.　Heavy　metals　in　wastewater　have　received　extensive　attention　because　of　their　non-degradability　and　biotoxicity.　In　order　to　apply　anammox　system　to　treat　wastewater　containing　heavy　metals　and　explore　the　anammox　system　recovery　to　complex　engineering　environments,　Ni(II)　was　used　as　representative　substance　to　investigate　its　long-term　effects　on　the　anammox　process　in　continuous　flow　reactors.　The　self-recovery　ability　of　the　anammox　system　after　long-term　exposure　to　Ni(II)　was　also　investigated.　The　results　showed　that　low　concentrations　of　Ni(II)　(＜=　5　mg/　L)　had　a　slight　inhibitory　effect　on　the　anammox　system,　while　high　concentrations　of　Ni(II)　(＞=　10　mg/L)　could　lead　to　the　deterioration　of　the　anammox　system.　Extracellular　polymeric　substance　(EPS)　content　increased　with　increasing　Ni(II)　concentration.　High-throughput　sequencing　results　showed　that　Ni(II)　severely　impacted　the　microbial　community　of　the　anammox　system,　especially　Candidatus　Kuenenia.　The　abundance　of　Candidatus　Kuenenia　decreased　from　32.11%　to　13.99%　with　increasing　Ni(II)　concentration　from　0　mg/L　to　15　mg/L.　After　stopping　Ni(II)　addition,　EPS　and　functional　bacterial　abundance　recovered　to　some　extent,　and　nitrogen　removal　efficiency　(NRE)　only　returned　to　44.53%　of　normal　levels.　The　self-recovery　of　the　anammox　system　was　a　longer　process.