The requirement of green technology is urgent for printed circuit boards (PCB). Not later to 2006, all the electronic products need meet green environment policy in Europe. In this paper, a novel and simple process to manufacture multilayer PCB was proposed. Follow our prior researches, base on the process of combining the self-assembly polyelectrolyte (SAP), ink-jet printing of catalyst, and electroless plating to form metal circuit pattern on the flexible substrate. This paper extended its application to fabricating of multi-layer flexible substrate. A double-sided flexible substrate with insulating material and connection holes was accomplished by this new improvement. By testing of IPC 6013 standard, the aspect ratio of thickness for metal foil and metal forming in hole was ideally near to one. In the impedance examination, the actual data was considerably closed to ideal data, within a variation of 0.4%. This improvement is helpful to fabricate high performance metal circuit on multilayer flexible substrate with holes.