Microorganisms can sense, resist, and respond to unfavorable environments (e.g., high salt stress). However, the microbial response mechanism to salt stress in anaerobic digestion (AD) remains poorly understood, especially quorum sensing (QS) and a two-component system (TCS). Salt stress disrupted the protein structure of loosely bound extracellular polymeric substance (EPS), which serve as protective barriers, and reduced the relative abundance of enzyme activities. Although methanogenic pathways were inhibited, acetoclastic methanogens (e.g., Methanosaeta) were selectively enriched with the addition of salt. Notably, genes related to QS and TCS were enhanced to resist salt stress, with a particular increase in the secretion of N-acyl-homoserine lactones. Batch tests on exogenous quorum strategies also verified the alleviating effect of QS on microorganisms against salt stress. Microbial metabolism associated with maintaining cell osmotic balance was also upregulated to cope with salt stress. This study elucidated the key roles of EPS, QS, and TCS in the response mechanism of microorganisms to salt stress, assisting in the development of bioprotective strategies.