To provide a method for manufacturing a thin film-bonded substrate, which can transfer a GaN thin film with high quality.

Ions are implanted from a Ga surface of a first GaN substrate up to a predetermined depth to form a first ion-implanted layer. A first heterogeneous substrate to be a substrate whose chemical composition is different from a first GaN substrate is bonded to the Ga surface of the first GaN substrate. The first GaN substrate is separated by using the first ion-implanted layer as a surface of separation and a second GaN substrate separated from the first GaN substrate is formed on the first heterogeneous substrate. Ions are implanted from an N face of the second GaN substrate up to a predetermined depth to form a second ion-implanted layer. A second heterogeneous substrate to be a substrate whose chemical composition is different from the second GaN substrate is bonded to the N surface of the second GaN substrate, the second GaN substrate and the first heterogeneous substrate are separated by using the second ion-implanted layer as a surface of separation and a GaN thin film separated from the second GaN substrate is formed on the second heterogeneous substrate.