In this paper, a modular architecture for system-on-chip design of scalable embedded MEMS actuator controller is presented. It addresses the contradiction between often large and expanding system function requirements and limited system resources, and provides a system level solution to solve this contradiction. A design methodology is developed to break the system function into multiple self-contained modules in case the above contradiction can not be solved in single chip design. A simple adaptive inter-modules/chip communications protocol is presented to maintain system integrity when modules/chips are added or removed.