The invention relates to the technical field of mechanical-electrical integration, in particular to a laser marking system and a positioning tool thereof. The positioning tool comprises a cutting workpiece tray and a workpiece positioning jig, the cutting workpiece tray is used for storing a thin film, and the workpiece positioning jig comprises a fixing base plate, a limiting device and a workpiece tray fixing device. The limiting device and the workpiece tray fixing device are both fixed to the fixing base plate. The workpiece tray fixing device comprises an adjustable portion, and the adjustable portion is matched with the limiting device to clamp two side faces of the cutting workpiece tray so as to stabilize the cutting workpiece tray. Compared with the prior art, the thin film is fixed to the top face of a lower die, and an upper die is fixed to the position above a film piece; when the positioning tool is utilized to position the thin film, after the thin film is placed on the cutting workpiece tray, the thin film is cut and formed, and cutting of a guide pinhole can be achieved; and manual alignment of the upper die and the lower die is not needed, accordingly the production efficiency is improved, and the automation degree is raised.