In order to make reconstruction of re-configurable manufacturing system (RCMS) more efficient and fast, a new design method for control structure and system layout is put forward. First, a holon control structure, such as centralized-control, hierarchical control, non-strictly hierarchical control, and distributed control, is introduced. Each function module of the control structure not only has relative independent character and also cooperation with other control structure. It may constitute the required structural according to the market demand at any time to realize re-configurable control goals. At last, the key technology and the implementation method involved in layout design of equipment and system layer are discussed.