The biodegradable controlled-release system with large array of micro chambers is a new controlled drug delivery system. The structure of the system is designed using the MEMS technology, combining the drug release condition and the biodegradable characteristic of the polymer. This type of drug delivery system has some unique advantages in controlled long-term drug delivery, such as more drug loading than the matrices release systems, easier control the release rate, and so on. It is necessary to optimum the structure for the long-term drug delivery. This paper founds the simulated modeling which can simulate the erosion and the drug delivery from this controlled-release system. Further more the thickness of the chamber's wall is taken as the design variable. An optimized modeling for the drug delivery from the biodegradable controlled-release system is developed. This model can optimize the structure of the controlled release system for the desired release characteristics. The results indicate that this method can be used to design the drug delivery system based on the biodegradable polymer.