A system partition method based on modular theory for EMUs was presented. By considering the basic properties of EMUs components function and application, with the relevant relations definition among components, a comprehensive relation matrix was acquired through analytic hierarchy process, and a mathematical system clustering model was established. Additionally, system partition results applicable to reliability analysis of EMUs were given by population genetic algorithm and MATLAB simulating calculation. The feasibility and effectiveness of this algorithm was verified according to sensitivity analysis, which provided basis for future research.