The present invention relates to an input method of a pointer input system. A setting procedure and a correcting procedure having been performed on the pointer input system to obtain a space conversion relationship and an over-bright position. The input method includes steps of inputting at least a light spot into a projection screen, capturing the light spot by a photosensing system to obtain a light-spot image, recognizing at least a relevant light spot of the light-spot image by checking whether the light-spot image excluding the over-bright position complies with a light-spot characteristic situation so as to obtain at least a light-spot data, and converting the at least a light-spot data into at least an input data of a data processing system according to the space conversion relationship.