In view of the existing chromatism in the AOTF multispectral imaging system causes different wavelength imaging clarity under different focal length , even under the fixed wavelength, due to the horizontal direction (diffraction) spectral broadening, which leads to clear horizontal lines and blurring vertical lines. This paper made a concrete analysis of the chromatism of AOTF, pointing out the causes of imaging blurring. According to the imaging characteristics of AOTF multispectral imaging system, this paper proposed an improved algorithm based on SSIM, which can be used to evaluate the image sharpness. The target of the original algorithm was two images (one as a reference image, the other one as the test image), while the algorithm proposed in this paper made similarity analysis between the adjacent lines in one target image, small similarity in change edges declares great contrast, thus the image is clearer. The image quality caused by chromatism in the AOTF multispectral imaging system can be compensated by automatic focusing system, which mainly based on this algorithm. It has small calculated amount and fast speed. The feasibility and practicability of the compensation strategy were verified through experiments. The results show that this strategy can effectively solve the image blurring caused by chromatism in the AOTF multispectral imaging system, which has an important application value.