Al13 and Al30 are the dominant aluminum (Al) species in polyaluminium chloride commonly used for sludge dewatering. However, the presence of extracellular polymeric substances (EPS) in the waste activated sludge hinders the coagulation effectiveness of Al-based coagulants. This study focused on the effects and mechanisms of Al13 and Al30 on treating sludge EPS. From a bulk perspective, the dosing of two coagulants significantly reduced the dissolved organic carbon and various organic compounds, reflecting their efficacy in removing organic substances in EPS. Further molecular characterization was revealed by FT-ICR MS. Al13 was more effective in removing lipids, lignins, and sulfur-containing compounds compared to Al30. Al13 also demonstrated a pronounced removal in components enriched in oxygen atoms (10–20) and KMD(COO) (0.5–0.7), suggesting its ability to remove molecules across a broader range of unsaturation. After coagulation with Al13, the areas corresponding to Al2p1/2 and Al2p2/3 in the Al2p spectra were more prominent compared to those in the Al30-coagulated EPS. Therefore, Al13 can both remove complex and low molecule weight compounds through abound forms of adsorption sites, making it more efficient in releasing bound water compared to Al30.