During advanced oxidation treatment for enhancing sludge dewaterability, the peptide chains of protein can be decomposed into amino acids. Protein exhibits a great impact on sewage sludge dewaterability. However, the role of amino acids in sludge dewatering remains unclear. In this study, among the 23 types of amino acids investigated, tryptophane (Trp) and lysine (Lys) were identified as the key amino acids affecting sludge dewaterability during Fenton oxidation treatment. The content of lysine showed positive correlations with capillary suction time (CST), specific resistance to filtration (SRF), and bound water content, and the concentrations of total protein, low molecular weight protein, amines and amides, and 3-turn helix of proteinaceous compounds in bound extracellular polymeric substances (EPS), while the content of tryptophane showed negative correlations with the above parameters. The amino acids may be sourced from damage of the membrane and ribosomal proteins by hydroxyl radicals, and the peptide bonds connected with tryptophane were more inclined to be decomposed than other amino acids. Particularly, more amino acids of tryptophane can result in more hydrophobic interaction, and less necessary energy barrier for aggregation of particles. As such, regulating protein degradation towards production of tryptophane may be related with enhanced sludge dewaterability by Fenton oxidation treatment.