Based on analyzing the mechanism of the Hyper-Spectral CCD Imager's non-uniformity and several non-uniformity correction algorithms. The method of two-point multi-section for Hyper-Spectral CCD Imager's non-uniformity correction was presented. The two-point multi-section method has higher precision than two-point correction algorithm and has lower operation load than multi-point correction algorithm. The appliance of the two-point multi-section method to Hyper-Spectral Imager showed that the method has the merit of low operation load,high precision and strong practicability.