Module partition of Complex product system (CoPS) usually produces a number of schemes, and how to choose the best one amongst the themes is very important. In this research, according to the features of CoPS, the multi-level evaluation indexes are built based on the DFX (design for X) method, which can evaluate the scheme comprehensively. The weight of indexes are obtained with the method of analytical network process. Then, the multi-level grey fuzzy comprehensive evaluation method is proposed to make the well-chosen decision based on the DFX multi-objective evaluation model. The evaluation method are illustrated using the partition schemes of the experiment platform of a bevel gearbox.