A multi-layer bonding method of the present invention includes: forming a first bonded substrate by bonding a first substrate and an intermediate substrate in a bonding chamber; conveying a second substrate inside said bonding chamber when said first bonded substrate is arranged inside said bonding chamber; and forming a second bonded substrate by bonding said first bonded substrate and said second substrate in said bonding chamber. According to such a multi-layer bonding method, the upper-side substrate can be bonded with an intermediate substrate and then a first bonded substrate is bonded with a lower-side substrate without taking out the first bonded substrate from the bonding chamber. For this reason, a second bonded substrate can be produced at high speed and at a low cost.