Method of manufacturing multilayer substrate

A method of manufacturing a multilayer substrate, the method comprising:

• preparing a plurality of substrates;
• stacking the substrates with bonding sheets interposed;
• and
• a first bonding process of bonding the substrates to each other by partially heating the stacked substrates by a heater and partially melting the bonding sheets, wherein:
• each of the substrates is provided with a through-hole and a metal film covering an inner peripheral surface of the through-hole;
• and
• in the first bonding process, the metal film on an outermost substrate is heated by the heater and heat is transferred from the heater to the bonding sheet adjacent the outermost substrate via the metal film, wherein:
• the heater has a heater head;
• in the first bonding process, the heated heater head is brought into contact with a region including the through-hole of the outermost substrate,
• the heater head is provided with a contact surface and a protruding portion protruding from the contact surface;
• and
• in the first bonding process, when the heater head is brought into contact with the region including the through-hole, the contact surface comes into contact with the substrate or the metal film, and the protruding portion is disposed in the through-hole.