A method of manufacturing a bonded substrate stack includes a bonding surface processing step of processing at least one of first and second substrates each containing silicon and having a bonding surface, and a bonding step of bonding the bonding surface of the first substrate and the bonding surface of the second substrate. The bonding surface processing step includes an OH group increasing step of increasing OH groups on the bonding surfaces, and a moisture content decreasing step of heating the bonding surfaces where the OH groups have been increased at a temperature falling within a range of 50° C. to 200° C. to decrease moisture contents of the bonding surfaces.