A five-step method framework is proposed by combing improved value stream mapping with simulation and design of experiment (DOE) to design the lean system for engineer-to-order (ETO) manufacturing, and lean practice implementation path is decided. Meanwhile, a real company case like HAVC is taken to display the application of the framework. The results indicate that compared to supermarket Kanban, constant work in process (Conwip) has the broader applicability in ETO manufacturing and the critical business process, like purchasing of key parts, and has more significant effects on value stream performance. Therefore, it should have priority in lean practice implementation. © 2016, Shanghai Jiaotong University and Springer-Verlag Berlin Heidelberg.