A thin section preparing apparatus prepares a thin section from an embedded block having a biological sample embedded and carries the thin section. The thin section preparing apparatus includes a cutter, an approaching and separating mechanism, a carrying mechanism, a moving unit, a sliding mechanism and a control unit. The cutter slices the block at a pull angle. The approaching and separating mechanism relatively moves the block and the cutter along an approaching and separating direction. The carrying mechanism having a carrying body is arranged as one end side is near a nose, and the moving unit moves the body along a transport direction. The sliding mechanism relatively moves the block and the body along a moving direction. The control unit controls a combined velocity vector that combines a transport velocity vector of the body along the transport direction with a travel velocity vector of the body along the moving direction to be nearly equal to a block velocity vector of the embedded block along the approaching and separating direction.