Quorum sensing (QS) signalling has been extensively studied in single species populations, activated sludge, biofilm and aerobic granular sludge. However, ecological roles of QS in anaerobic granular sludge, particularly in the content of the relationship between QS signalling and microbial community composition and function, have been rarely reported. Herein, five acyl-homoserine lactones (AHLs) molecules were added in the anaerobic granular sludge system for treating traditional Chinese medicine (TCM) wastewater respectively. The results indicated that the introduction of specific AHLs could enhance the abilities of organic matters removal and methanation in anaerobic granular sludge, and meanwhile, exogenous AHLs played an important role to regulate the concentration of EPS. Sequencing analysis indicated that microbial community structures of bacteria and methanogens changed to varying degrees by adding AHLs. This study suggested that exogenous AHLs could play a role in mediating microbial community structure, thereby enhancing the performance of anaerobic granular sludge. The regulatory mechanism of AHLs on community structure was discussed, and a speculative action model was established. Exogenous regulation by selective enhancement of AHLs-mediated QS in anaerobic granular sludge provided an innovative and attractive strategy for strengthening wastewater treatments.