An automatic thin section sample preparation device includes: a reading portion which reads the ID data； a first imaging portion which images a surface image of an embedding block； a sample preparation mechanism which prepares a thin section by thinly cutting the embedding block, fixes the thin section to a substrate, and prepares a thin section sample； a second imaging portion which images a thin section image of the thin section in the thin section sample； a recording portion which records individual data on the substrate in the thin section sample； and a control portion. The control portion includes a determination portion which determines whether or not the thin section is prepared from an original embedding block by collating the surface image and the thin section image, and a storage portion which stores the determination result from the determination portion in association with the ID data, as the individual data.
