There is provided a charged particle beam system in which a detector can be placed in an appropriate analysis position. The charged particle beam system (100) includes: a charged particle source (11) for producing charged particles; a sample holder (20) for holding a sample (S); a detector (40) for detecting, in the analysis position, a signal produced from the sample (S) by impingement of the charged particles on the sample (S); a drive mechanism (42) for moving the detector (40) into the analysis position; and a controller (52) for controlling the drive mechanism (42). The controller (52) performs the steps of: obtaining information about the type of the sample holder (20); determining the analysis position on the basis of the obtained information about the type of the sample holder (20); and controlling the drive mechanism (42) to move the detector (40) into the determined analysis position.