The　widespread　occurrence　of　heavy　cyanobacterial　blooms　has　posed　serious　threats　to　aquatic　ecosystem　and　human　health.　In　this　work,　a　novel　Z-scheme　Ag3PO4@PANI　core–shell　photocatalyst　was　synthesized　by　a　chemisorption　method　for　Microcystis　aeruginosa　(M.　aeruginosa)　inactivation.　The　crystal　structure,　morphology,　chemical　states,　and　optical　properties　of　as-prepared　samples　were　characterized　by　XRD,　TEM,　XPS,　ATR-FTIR,　NMR,　UV–vis,　and　PL.　Ag3PO4@PANI　with　10　wt.%　of　PANI　showed　the　best　performance　of　photocatalytic　algae　removal　with　99.2%　chlorophyll　a　degradation　under　3　h　visible　light　irradiation　and　excellent　photostability　after　repetitive　three　times　cyclic　experiments.　Moreover,　the　changing　conditions　of　M.　aeruginosa　physiological　characteristics　during　photocatalytic　process　were　investigated.　Furthermore,　quenching　experiment　results　indicated　that　superoxide　radicals　(·O2−)　and　photoinduced　hole　(h+)　were　dominant　reaction　active　species.　Finally,　the　possible　inactivation　mechanism　of　M.　aeruginosa　was　proposed.　Overall,　this　study　provides　a　new　insight　in　the　efficient　removal　of　the　algae　pollutants　in　eutrophic　water　bodies　using　Z-scheme　mechanism　core–shell　photocatalysts.　©　2021　Elsevier　B.V.