A pointer positioning system includes an image generating unit, a light-spot generating unit, an operating unit, a calculating unit, and an image unit. The image generating unit creates an image on a display region. The light-spot generating unit projects positioning spots and identifying spots on the display region. The operating unit has an invisible-light camera to sense an image of a part of the entire display region. The calculating unit compares a distribution of the positioning spots and the identifying spots which is sensed by the invisible-light camera with a reference distribution stored in a memory, and the image unit shows a pointer image at a pointing position of the display region accordingly.