An augmented reality training system, comprising: a manipulation platform, having a model-placement area for placement of a surgical phantom and a workspace for permitting a user to perform manipulation training on the surgical phantom; an augmented reality stereo microscopic assembly, being disposed in relation to the manipulation platform and configured for camera-based capture of real stereo videos of the surgical phantom and an instrument to be manipulated on the surgical phantom and for transmission of augmented reality images into the user's eyes; an instrument tracking module, including at least one top digital camera and at least one bottom digital camera and being configured to provide three-dimensional position and orientation signals of the instrument, wherein the top digital camera is disposed above the workspace to track a marker at an upper portion of the instrument, and the bottom digital camera is disposed below the workspace to track a lower portion of the instrument; and a simulation generation module, including a processor being coupled to the augmented reality stereo microscopic assembly and the instrument tracking module and configured to generate and display the augmented reality images that merge the real stereo videos from the augmented reality stereo microscopic assembly and virtual images based on the three-dimensional position and orientation signals and a training program for simulation of actions of the instrument in interaction with the training program; wherein the virtual images include a virtual pupil area and at least one virtual object which are generated based on the training program, the at least one virtual object is in interaction with the instrument, and the processor is configured to record a result, which includes the three-dimensional position and orientation signals of the instrument and the virtual images, in the training program for evaluating the user's skill. a manipulation platform, having a model-placement area for placement of a surgical phantom and a workspace for permitting a user to perform manipulation training on the surgical phantom; an augmented reality stereo microscopic assembly, being disposed in relation to the manipulation platform and configured for camera-based capture of real stereo videos of the surgical phantom and an instrument to be manipulated on the surgical phantom and for transmission of augmented reality images into the user's eyes; an instrument tracking module, including at least one top digital camera and at least one bottom digital camera and being configured to provide three-dimensional position and orientation signals of the instrument, wherein the top digital camera is disposed above the workspace to track a marker at an upper portion of the instrument, and the bottom digital camera is disposed below the workspace to track a lower portion of the instrument; and a simulation generation module, including a processor being coupled to the augmented reality stereo microscopic assembly and the instrument tracking module and configured to generate and display the augmented reality images that merge the real stereo videos from the augmented reality stereo microscopic assembly and virtual images based on the three-dimensional position and orientation signals and a training program for simulation of actions of the instrument in interaction with the training program; wherein the virtual images include a virtual pupil area and at least one virtual object which are generated based on the training program, the at least one virtual object is in interaction with the instrument, and the processor is configured to record a result, which includes the three-dimensional position and orientation signals of the instrument and the virtual images, in the training program for evaluating the user's skill.