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 (N-octanoyl-l-homoserine lactone, C8), 3-oxo-AHLs (3-oxo-octanoyl)-l-homoserine lactone, 3-oxo-C8), and AHLs analogs (γ-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. β-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.