A biodegradable controlled drug release microstructure with an array of micro chambers is a new kind of controlled drug delivery system which is made by biodegradable polymer. For a certain desired drug release profile, it is necessary to optimize the structure of the polymer device. In this study, a new mathematical model for a biodegradable controlled drug delivery system is presented by using Cellular Automata (CA). Furthermore, the simulations of the biodegradable controlled-release system with an array of micro chambers with different structures are carried out. By a structural optimization (optimal non-uniform distribution and dimension), a desired drug release profile is achieved. In conclusion, the study introduced here is important for the structural optimization design of the biodegradable controlled-release system with large array of micro chambers.