A method for manufacturing a bonded substrate that has an insulator layer in part of the bonded substrate includes: partially forming a porous layer or forming a porous layer whose thickness partially varies on a bonding surface of the base substrate; performing a heat treatment to the base substrate having the porous layer formed thereon to change the porous layer into the insulator layer, and thereby forming the insulator layer whose thickness partially varies on the bonding surface of the base substrate; removing the insulator layer whose thickness varies by an amount corresponding to a thickness of a small-thickness portion by etching; bonding the bonding surface of the base substrate on which an unetched remaining insulator layer is exposed to a bond substrate; and reducing a thickness of the bonded bond substrate and thereby forming a thin film layer.