An algorithm for a sharpness evaluation of microscopic images based on non-subsampled shearlet wave transform (NSST) and variance is proposed in the present study for the purpose of improving the noise immunity and accuracy of a microscope’s image autofocus. First, images are decomposed with the NSST algorithm; then, the decomposed sub-band images are subjected to variance to obtain the energy of the sub-band coefficients; and finally, the evaluation value is obtained from the ratio of the energy of the high- and low-frequency sub-band coefficients. The experimental results show that the proposed algorithm delivers better noise immunity performance than other methods reviewed by this study while maintaining high sensitivity.