According to one embodiment, there is provided a substrate bonding apparatus including a first chucking stage, a second chucking stage, and an alignment unit. The first chucking stage is configured to chuck a first substrate. The second chucking stage is disposed facing the first chucking stage. The second chucking stage is configured to chuck a second substrate. The alignment unit is configured to be inserted between the first chucking stage and the second chucking stage. The alignment unit includes a base body, a first detection element, and a second detection element. The base body includes a first main face and a second main face opposite to the first main face. The first detection element is disposed on the first main face. The second detection element is disposed on the second main face.