A microscope system stores, for each objective, the movement control information including a type flag indicating the type of an objective depending on the presence/absence of a soak or a type of the soak and a save distance for saving the stage or the objective switch unit by a predetermined distance. When a switch direction of objectives is input, and when there is a change in the type of the objective after the switch, the system stops an operation after the stage or the objective switch unit is moved according to the save distance, and recovers the stage or the objective switch unit to an original position after the operation direction input unit inputs an operation direction for the stage and the objective switch unit.