The invention provides an optical confocal three-dimensional data acquisition method of tool traces, and the acquisition system comprises a microscope, a digital imaging device, a mobile control module and an image fusion device, wherein, the microscope comprises a microscope carrier, a microscope optical system and a microscope vernier adjustment knob, the digital imaging device is arranged above the microscope optical system and used for acquiring images, the mobile control module is connected with the microscope vernier adjustment knob and used for regulating the movement of the microscope optical system, and the image fusion device receives the sequence of the images collected by the digital imaging device, extracts clear parts in all the images and fuses into a full-clear image.