The extracellular polymeric substances (EPS) are important macromolecular components in microbial aggregates. The three EPS extraction methods – ultrasound + cation exchange resins (CER) + sulfide, ultrasound + formamide + NaOH, and ultrasound + heat – were investigated in the study, and the component differences of extracted EPS from the loose flocs and dense aerobic granules were compared using chemical analysis and three-dimensional excitation-emission matrix (3D-EEM). Results showed that the contents of EPS were extracted effectively by ultrasound + formamide + NaOH and ultrasound + heat methods, and the ultrasound + CER + sulfide method did not extract the polysaccharides (PS) or protein (PN) contents from the sludge samples. The 3D-EEM analysis indicated that the nature of peak B/D, peak C/E/F, and peak A/G were attributed to PN-like, humic acid-like and fulvic acid-like fluorophores. All fluorophores can be detected from the EPS extracted through the ultrasound + heat method. Hopefully this will provide more information about the EPS interaction mechanism of microbial aggregates.