Aiming at the problem of grayscale difference in multispectral images of aerial filter array, a new method of the strip grayscale correction algorithm is proposed in this paper. Firstly, the strip image template was constructed for multispectral image, and the scale invariant feature transform algorithm was used to extract image feature points and calculate inter-image coordinate transformation matrix, which was used to determine the overlap region of strip image. Secondly, the mean value of the greyscale of pixels in the overlapping area of each strip image was calculated, and the greyscale correction coefficients between adjacent images were fitted with the greyscale of each strip of greyscale intermediate image as a reference. Finally, the projected image templates were used to extract sequential single-band strip in turn and stitch them together to obtain a single-band image with same greyscale. Experimental results show that this method can effectively solve the difference in the greyscale of multispectral image strips of aerial filter array, and can maintain the maximum spectral information characteristicsof the ground feature.