A self-organizing fuzzy controller is constructed for control of substrate concentration in fed-batch operation of a cell culture process. A genetic algorithm is used to generate fuzzy rules of the self-organizing fuzzy controller and to modify the universe of discourse automatically. The fuzzy controller is designed for the application of Scutellaria baicalensis G. plant cell culture process as a model system. A substrate feeding strategy of a two stage culture method to maximize flavone glycoside production in fed-batch culture of Scutellaria baicalensis G. plant cell is proposed based on structured model of growth and product synthesis. As a two stage culture, the feeding strategy consists of the first period at 22 g/L of glucose concentration to promote cell growth and the second period at 10 g/L of glucose concentration to promote flavone glycoside synthesis. The designed self-organizing fuzzy controller is applied to regulate the glucose concentration at a given set-point to increase flavone glycoside synthesis. The simulation results show that the proposed feeding strategy in a fed-batch culture enhances flavone glycoside production and the self-organizing fuzzy logic controller generated by genetic algorithm improves controller performance.