Provided are an image difference-based method and system for tracking a transparent object, first by training a convolutional neural network based on sample data, to generate a transparent object detection model; then inputting visible light image data acquired in real time and infrared thermal image data acquired in real time to the transparent object detection model, to acquire a visible light image transparent pixel identifier and an infrared thermal image transparent pixel identifier; then calculating three-dimensional point cloud information of each pixel marked by the infrared thermal image transparent pixel identifier, in the infrared thermal image data, wherein the three-dimensional point cloud information is in a coordinate system of an infrared thermal imaging camera; wherein the infrared thermal imaging camera is a camera for acquiring the infrared thermal image data, thereby acquiring, according to the three-dimensional point cloud information, corresponding position coordinates of each pixel, which is marked by the infrared thermal image transparent pixel identifier, in the visible light image data, and fitting the position coordinates with the visible light image transparent pixel identifier, to acquire tracking information of the transparent object.