This study investigated the effect of three common quorum sensing signal molecules on anaerobic granular sludge (AnGS) in unbalanced nitrogen supply. Oligotrophic nitrogen supply transiently increased the level of N-butanoyl-homoserine lactone (C4-HSL), maintaining the stability of granules by encouraging synthesis of loosely bound extracellular polymeric substance (LB-EPS). Meanwhile, the decreasing autoinducer-2 (AI-2) content and increasing diffusible signal factor (DSF) content made a combined effect on AnGS, and then it recombined the regulation from N-acyl-homoserine lactones (AHLs). In addition, eutrophic nitrogen supply enhanced C4-HSL and N-hexanoyl-homoserine lactone (C6-HSL) secretion, suggesting that it increases loose bound protein (LB-PN) level to survive in the suppression of nitrogen supply. During the unbalanced nitrogen supply process, the weaker positive effect of AI-2 and enhanced negative effect of DSF reduced relative hydrophobicity (RH) and granular strength, which made a decline of granular diameter and a degeneration of granular sludge in nitrogen oligotrophic reactor (OR) and nitrogen eutrophic reactor (ER). Therefore, the effect of the interactions among multiple signal molecules should be further elucidated in future study.