A novel assembly method for a micro direct methanol fuel cell (μDMFC) using multi-layer bonding is developed. The anode and cathode plates of the μDMFC are fabricated by using MEMS technologies. PDMS gaskets are introduced to fill the gap between the silicon plate and the membrane electrode assembly (MEA) to prevent fuel or oxidant leaking. To assemble a μDMFC, adhesive tapes and oxygen plasma treatment of the PDMS gasket for surface activation are introduced. In this method, the PDMS gasket with adhesive tapes is bonded to the silicon plate then bonded to the MEA, which fixes the movable components of the μDMFC to simplify the assembly operation. The novel assembly method shows good maneuverability and reliability. The μDMFC shows great performance due to the low internal resistance attributing to this novel assembly method. With thermal insulated holders, the μDMFC generates a power density of 20.29mW/cm2. This assembly method is applicable for the assembly of the μDMFC stack.