As　a　type　of　quaternary　ammonium　compounds,　didodecyl　dimethyl　ammonium　chloride　(DADMAC　C12)　was　frequently　detected　in　wastewater　treatment　plants.　Here,　floc-based　sequencing　batch　reactor　(FSBR),　granule-based　SBR　(GSBR)　and　biofilm　SBR　(BSBR)　were　fed　with　0.5,　5　and　10　mg/L　of　DADMAC　C12　for　120　d.　Compared　with　floc　sludge　and　granule　sludge,　biofilm　had　the　strongest　ability　to　resist　the　impact　of　DADMAC　C12.　Notably,　in　both　FSBR　and　GSBR　systems,　5　mg/L　DADMAC　C12　promoted　denitrification　sludge　to　become　hydrophobic　and　compact　due　to　an　increase　in　α-Helix/(β-Sheet+Random　coil),　consequently　enhancing　sludge　granulation.　Besides，high　concentration　of　DADMAC　C12　generally　increased　the　abundances　of　MGEs　in　three　denitrification　systems,　except　extracellular　MGEs　in　water.　The　variation　of　efflux　pump　ARGs　was　basically　consistent　with　that　of　MGEs.　The　stimulation　of　DADMAC　C12　also　increased　significantly　the　abundance　of　extracellular　antibiotics　deactivation　ARGs　in　water　in　three　denitrification　systems.　Besides,　DADMAC　C12　induced　co-selection　among　various　ARGs　and　promoted　the　proliferation　and　spread　of　sulfonamide　ARGs　in　water.　©　2023　Elsevier　B.V.