In a pointing input system and method, a pointer applies a light spot on a screen, an array sensor shoots on the screen to generate a first data for an identification system to retrieve a second data therefrom, the second data includes the position information of the light spot for an information system to apply a correlated output on the screen. The second data is generated based on an optical distortion information and a spatial rotation and displacement information determined by an alignment procedure that comprises applying an input for alignment on the screen for the array sensor to shoot to generate an alignment data, and comparing the alignment data with a reference data.