A multilayer substrate is manufactured by first manufacturing a first substrate by stacking and hot-pressing resin base materials of the first substrate and then adjacently stacking and hot-pressing the first substrate and resin base materials that constitute a second substrate at a position overlapping with each other in a stacking direction. The position in the stacking direction between the resin base materials in the first substrate is located at almost a middle position in the stacking direction of a resin base material of the second substrate, and is different from the position between the layers of the resin base materials of the second substrate.