A multispectral imaging system acquires spectral color images by splitting the light spectrum into multiple bands. Due to the different refractive index for individual wavelength, the focus positions of the channels are different, and thus each channel should be adjusted to obtain sharp image. We propose a fast autofocus method based on the similarity of focus measure distributions, which is suitable to multispectral imaging. In the proposed method, we first obtain the focus measure distribution of a reference channel using traditional autofocus method. Then, the clear focus positions of other channels are located according to the distribution similarity between individual channels. As only a few images are needed, the autofocus for these channels is quite fast. Experimental results validate that the proposed method performs better than the traditional techniques.