A method for manufacturing a silicon-on-insulator substrate, comprising: forming an oxide film in at least a surface of an active layer-forming substrate including a single-crystal semiconductor; implanting hydrogen ions from the surface of the active layer-forming substrate so as to form an ion-implanted region within the active layer-forming substrate; subjecting the active layer-forming substrate to a first heat treatment in a state in which the active layer-forming substrate contacts, through the oxide film, with a base substrate including a single-crystal semiconductor so as to separate the active layer-forming substrate from the base substrate at the ion-implanted region and form an active layer on a surface of the base substrate, thereby, forming a bonded substrate; measuring film thickness throughout the active layer; generating reactive ions and reactive radicals by a plasma etching process, separating the reactive ions from the reactive radicals, and selectively using only the reactive radicals to etch the surface of the active layer based on a film thickness data obtained by the measuring of the film thickness, in such a way as to etch off at least 100 nm of the active layer and thin the active layer so that the thickness of the active layer is in a range of 10 to 200 nm, and the thickness variation throughout the active layer after plasma etching is 1.5 nm or less; additionally plasma-etching a boundary area between an inactive region and an active region at a periphery of the bonded substrate by a thickness equal to that of the active layer prior to the plasma etching, based on the film thickness data; and subjecting the plasma-etched bonded substrate to a second heat treatment so as to enhance the bond strength. forming an oxide film in at least a surface of an active layer-forming substrate including a single-crystal semiconductor; implanting hydrogen ions from the surface of the active layer-forming substrate so as to form an ion-implanted region within the active layer-forming substrate; subjecting the active layer-forming substrate to a first heat treatment in a state in which the active layer-forming substrate contacts, through the oxide film, with a base substrate including a single-crystal semiconductor so as to separate the active layer-forming substrate from the base substrate at the ion-implanted region and form an active layer on a surface of the base substrate, thereby, forming a bonded substrate; measuring film thickness throughout the active layer; generating reactive ions and reactive radicals by a plasma etching process, separating the reactive ions from the reactive radicals, and selectively using only the reactive radicals to etch the surface of the active layer based on a film thickness data obtained by the measuring of the film thickness, in such a way as to etch off at least 100 nm of the active layer and thin the active layer so that the thickness of the active layer is in a range of 10 to 200 nm, and the thickness variation throughout the active layer after plasma etching is 1.5 nm or less; additionally plasma-etching a boundary area between an inactive region and an active region at a periphery of the bonded substrate by a thickness equal to that of the active layer prior to the plasma etching, based on the film thickness data; and subjecting the plasma-etched bonded substrate to a second heat treatment so as to enhance the bond strength.