We have developed a microscopic adaptive optics (AO) system that corrects wavefront phase errors induced by complex structures of biological samples. The technique of correlation-based Shack-Hartmann (SH) sensing used in the AO system enables wavefront measurement using complex structures in a target as the reference. However, sub-images in the SH sensor become deformed dependently on the positions of sub-apertures as the NA of the microscopic objective is higher. This often deteriorates the accuracy of wavefront sensing. To mitigate the undesirable effect, we here propose a differential wavefront sensing technique with a mathematical formula, which is expected to measure wavefront at a better precision. Because differences in image shapes are less significant between nearby SAs, correlations between adjacent SAs are measured in the proposed method. We confirmed that the AO system worked as designed by experiments.