Substrates are aligned and then bonded to each other. A substrate bonding apparatus includes a deformer that deforms at least a first one of two substrates that are to be bonded to each other in order to correct misalignment between the two substrates, a holder that holds the deformed first substrate in the deformed state achieved by the deformer, a transporter that transports the holder from a position at which the deformed first substrate is held by the holder while the first substrate remains deformed, and a bonder that bonds the first substrate that has been transported by the transporter to the second substrate. In the above-described substrate bonding apparatus, while the first substrate is not held by the holder, the deformer may deform the holder from a first state to a second state that is more deformed than the first state, and while the first substrate is held by the holder, the deformer may reduce the amount of the deformation of the holder to less than the amount of the deformation of the second state to deform the first substrate.
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