Stripe non-uniformity is a relatively common fixed pattern noise in infrared focal plane array imaging systems, which has a great impact on imaging quality. It is generally believed that the non-uniformity of an image is mainly reflected in the gray level difference between pixels, that is, the gray level difference caused by the non-uniformity. In order to solve this problem, a correction method of stripe non-uniformity based on gray difference estimation is proposed. According to the spatial characteristics of the strip noise, the position of the non-uniform strip in each frame is judged. According to the gray level difference between adjacent pixels at the position of the strip, the non-uniformity is preliminarily estimated, and the estimation results of the next frame are evaluated to further improve the estimated value. Experimental results show that the proposed method can significantly reduce fringe non-uniformity and can effectively protect the edge information of the image.