The pointer input system accomplishes a setting up routine and a correction program so as to obtain a relation of space transform and a position of over bright spot. The method includes following steps: inputting at least a light spot to a screen, and using a system of sensitizing device to shoot the screen so as to obtain image of a light spot; next, neglecting the location of the over bright spot in the image of the light spot, checking up the rest of satisfying condition of character of light spot in order to recognize at least a light spot corresponding to image of the light spot so as toobtain information of at least a light spot; then, under the relation of space transform, transforming the information of light spot into at least an input information in use for operating a information system.