A manufacturing method of a multilayer substrate that suppresses relative displacement of layers and forms interconnecting portions electrically connecting layers having an accurate positioning. A manufacturing method of a multilayer substrate for laminating, via an insulating film, a wiring layer formed by patterning a conductive film comprises providing a positioning hole in a conductive film laminated at the beginning and patterning a second and/or any subsequent wiring layers after identifying a position of an identification section. Interconnecting sections for interconnecting wiring layers are formed using the identification section.