An auto-focusing method used for the multi-spectral imagers was proposed based on differential projection. The method uses an image processing unit and auxiliary focusing equipment of sensors to implement the auto-focusing processes for different spectral bands separately and simultaneously. Firstly, the focusing window was delimited manually according to the observation needs or was searched automatically on the basis of the corresponding relations of differential projection and target edges. Then, the focusing window data of the image to be focused and calculated were projected in x-direction and y-direction, the 1st norm of the two projection arrays' first order differential values was derived and the mean of the two sets of 1st norm data was computed. Furthermore, the RMS of the two means was taken as the definition evaluation value of this image. Finally, combined with the classic mountain climb-searching method, the auto-focusing process was finished. Experimental results indicate that the auto-focusing method based on differential projection can be realized accurately, and it has the same effect with the classic Brenner, energy gradient and Roberts gradient algorithm, approximately. However, the running time of differential projection is only 0.67 times of Brenner, 0.33 times of Energy gradient, and 0.33 times of Roberts gradient. With the advantages of its strong single peak features, good unbiased characteristics, high sensitivity and excellent real-time, the method can meet the requirements of high-precision auto-focusing very well.