This paper briefly introduces the commonly used photoelectric auto collimator structure and its working principle. A new method for calibrating the initial point of collimator CCD imagine by a pyramid prism was proposed. It consists of a two-dimension rotate instrument, a pyramid prism and a collimator. By combing with the algorithm of calculating the center position of beam spot, a more precise calibration of the initial point of the collimator CCD imagine was realized. Optical properties of the pyramid prism and its impact of initial point calibration were analysed under the oblique incidence. At the same time, effect of the manufacturing errors of pyramid prism on the calibration accuracy was analysed. Experimental data shows that the method has a good reproducibility with a relative standard deviation of less than 10%.