There is provided a method for producing a bonded substrate comprising, at least, a process of joining two substrates and a process of subjecting the joined substrates to heat treatment to bond them firmly, wherein, at least, a process of cleaning for removing contaminants on the surface of the substrates is performed before joining the substrates, and then a process of drying the cleaned surface of the substrates is performed without using the water displacing method for the drying process, so that moisture is left on the substrates before joining to increase a joining strength after joining the substrates. Thereby, there can be provided a method for producing a bonded substrate wherein a joining strength of the joining interface of the substrates to be joined is improved, and thus the bonded substrate wherein there is no void failure and blister failure in the bonding interface of a bonded substrate after bonding heat treatment can be produced at high productivity and high yield.