PURPOSE: A bonded substrate manufacturing method is provided to reduce manufacturing costs and simplify manufacturing processes by easily bonding two different substrates while maintaining the quality of each substrate. CONSTITUTION: A bonded substrate manufacturing method is comprised of the following procedures. A first substrate and a second substrate are polished(S211). The polished first and second substrates are washed(S212). A bonded substrate is formed by bonding the first substrate and the second substrate(S213). The bonded substrate is cooled(S214).