A substrate holding device includes: holding members configured to hold substrates, the holding members being arranged along a predetermined arranging direction and being movable along the arranging direction; an interlocking mechanism interlocking the holding members for simultaneous coordinate movement along the arranging direction to change intervals between the holding members with respect to the arranging direction; driving unit for driving the holding members for shifting at least along the arranging direction; and control unit for controlling the driving unit to shift the holding members to substrate taking positions where the holding members are able to hold substrates, respectively, in accordance with a mapping information about a condition of arrangement of the substrates arranged along the arranging direction.