A method of manufacturing a multilayer substrate includes 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 sheet. Each of the substrates is provided with a through-hole and a metal film covering an inner peripheral surface of the through-hole. In the first bonding process, the metal film is heated by the heater and heat is transferred from the heater to the bonding sheet via the metal film.