Three-dimensional excitation-emission-matrix (EEM) fluorescence spectrometry was used to characterize the extracellular and intracellular substances of activated sludge in a sequencing batch reactor (SBR). Parallel factor analysis (PARAFAC) was applied to extract the pure spectra from the overlapped spectra. Three main components, proteins, fulvic- and humic-like substances, were identified from the extracellular substances. Their fluorescence peaks were at an excitation/emission (Ex/Em) of 280/350, 340/400 and 390/450 nm, respectively. The fluorescence of the extracellular proteins had a similar changing pattern with the wastewater chemical oxygen demand, the fulvic-like substance did not vary significantly in a cycle and the humic-like substances accumulated in the substrate uptake phase but decreased later. Proteins and nicotinamide adenine dinucleotide, reduced form (NADH), were identified as the two main intracellular fluorophores, and their fluorescence peaks (Ex/Em) were at 280/340 and 350/450 nm, respectively. The fluorescence intensity scores of the intracellular fluorophores were closely related to the bioreactor performance. Thus, the results of this work provide a foundation for potential utilization of the EEM fluorescence spectroscopy to monitor the activated sludge systems for wastewater treatment.