Two groups of sequencing batch reactors were used to study the metabolism substrate transformation of phosphorus-accumulating organisms (PAO) and glycogen-accumulating organisms (GAO) fed with mixed acetic and propionic acids. Seven stoichiometry parameters and 24 kinetic parameters were contained in the PAO and GAO kinetic model, and stoichiometry parameters were deduced from the stoichiometry models, while kinetic parameters were determined by experimental results. The kinetic model parameters of stoichiometry and kinetics were determined according the experiments and the literature. Subsequently, the substrate transformations of PAO and GAO were calculated by the Matlab software. The model curves matched the SBR experimental data well, indicating that the kinetic model based on SCFAs metabolism could be used to simulate PAO and GAO in anaerobic-aerobic conditions.