Bacteria and algae often coexist in the aerobic granular sludge (AGS) system in a photo-bioreactor, forming algal-bacterial granular sludge. In this study, the physicochemical characteristics and microbial attachment potential of the AGS and algal-bacterial granular sludge were comparatively analyzed. Results clearly showed that the larger and denser algal-bacterial granular sludge had stronger attachment potential compared to the AGS (as the control). A bioassay with Agrobacterium tumefaciens KYC55 indicated that N-acyl-homoserine lactones (AHLs) existed in both sludge types, but further investigations revealed that the relative AHL content of the algal-bacterial granular sludge obviously increased and slightly decreased during phases II and III, respectively, but was consistently higher than the AGS. Based on the EPS measurements and 3D-excitation-emission matrix (3D-EEM) fluorescence spectra analysis, the enhancement of AHL-based QS favored the hydrophobic protein production of algal-bacterial granular sludge, contributing to a good development of the granular sludge. In addition, it was also found that inhibition of AHLs resulted in the reduction of the protein content and attachment potential in algal-bacterial granular sludge, which was unfavorable to the structural stability of the granules. High-throughput sequencing analysis showed that the microbial community of AGS was different from the algal-bacterial granular sludge; specifically, algal-bacterial granulation facilitated the abundance of AHLs and EPS producers, such as the genera Acinetobacter, Chryseobacterium, and Flavobacterium.