A substrate holding device has a substrate holding unit and supporting elements movable to protrude from a substrate-holding surface of the substrate holding unit. The substrate holding unit holds the substrate in a predetermined state with a first holding force after relative positions of the substrate and the substrate holding unit are adjusted while the supporting elements lift the substrate off the substrate-holding surface. Before the relative positions of the substrate and the substrate holding unit are adjusted, the substrate holding device holds the substrate with a second holding force that is smaller than the first holding force and includes a zero holding force. Thus, the substrate holding device is able to align and hold the substrate in a short time.