Quorum　quenching　consortia　(QQC)　enriched　by　special　substrates　for　bioaugmentation　is　a　promising　QQ　technology　to　reduce　biofouling,　sludge　yield,　and　sludge　bulking.　However,　the　effect　of　substrate　type　on　the　performance　of　QQC　is　still　a　research　gap.　This　study　selected　three　different　substrates,　regular　AHLs　(Noctanoyl-l-homoserine　lactone,　C8),　3-oxo-AHLs　(3-oxo-octanoyl)-l-homoserine　lactone,　3-oxo-C8),　and　AHLs　analogs　(gamma-caprolactone,　GCL)　to　enrich　three　QQC　(C8-QQC,　3OC8-QQC,　GCL-QQC).　Combining　metagenomic　sequencing,　protein　prediction,　and　molecular　docking　to　fill　the　above　gaps　from　the　perspective　of　bacteria　and　enzymes.　The　performance　of　the　three　QQC　decreased　with　the　increasing　complexity　of　the　molecular　structure　of　the　substrates.　This　decline　was　attributed　to　more　complex　substrate　enriched　with　more　bacteria,　lacking　QQ　genes　in　the　QQC.　All　QQC　degraded　N-acetyl-l-homoserine　lactones　(AHLs)　via　acylase　and　lactonase.　C8-QQC　and　3OC8-QQC　showed　stronger　degradation　capabilities　for　N-(3-oxo-hexanoyl)-L-homoserine　lactone　(3OC6)　compared　to　N-hexanoyl-L-homoserine　lactone　(C6),　whereas　GCL-QQC　exhibited　stronger　degradation　for　C6.　Molecular　docking　results　showed　that　in　3OC8-QQC　and　C8-QQC,　most　enzymes　exhibited　stronger　degradation　capabilities　for　long-chain　and　3OAHLs.　However,　in　GCL-QQC,　more　QQ　enzymes　showed　stronger　degradation　for　C6　than　for　3OC6,　explaining　the　observed　differences　in　AHL　degradation.　beta-Oxidation　metabolic　pathways　in　bins　revealed　differences　in　their　abilities　to　metabolize　octanoic　acid　from　C8　and　3-oxo-octanoic　acid　from　3OC8,　which　influenced　their　abundance　in　the　respective　QQC.　The　study　findings　offer　insights　into　the　relationship　between　substrates　and　QQC　performance　at　the　gene　and　protein　levels.