This research endeavored to elucidate the influence of elastic fillers on the performance and archaeal community configuration of the Anaerobic Baffled Reactor (ABR). Utilizing high-throughput sequencing technology, the archaeal community structure was assessed in two distinct ABR sets. The findings revealed that the introduction of elastic fillers led to an enhancement in the average COD removal rate, BOD5 removal rate, effluent biodegradability, and fecal coliform removal rate of the ABR by 3.55%, 3.02%, 7.45%, and 96.85% correspondingly. Concurrently, it facilitated the transformation and degradation of organic matter within the ABR, thus resulting in an increased conversion of organic matter into Volatile Fatty Acids (VFA) within the initial compartment, and enhanced VFA degradation in the subsequent compartments. Indices such as Chao1, Observed species, Simpson, and Shannon concurred that the abundance and heterogeneity of the archaeal community within the ABR were augmented. The average relative abundance of dominant archaea (Methanosaeta and Methanobacterium) in the first compartment of ABR diminished by 3.44%, whereas in the second, third, and fourth compartments, the abundance escalated by 10.50%, 4.18%, and 2.78% respectively. The inclusion of elastic fillers not only amplified the hydrolysis and acid production process in the first compartment of the ABR but also fostered the methane production process in the subsequent compartments.