Abstract: In order to solve the problem of phase distortion in the micro size (1 mm) transmitting objects measurement based on digital holographic microscopy, a new correction method was proposed. By improving the pre-amplification off-axis Fresnel digital holographic recording system and convolution reconstruction algorithm, the phase distortion including both one-fold and two-fold had been corrected. In the experiment, the phase distortion of USAF1951 resolution board was corrected, and the 3D image of phase distribution of part of the board with size of 0.25 mm was clearly reconstructed. The advantage of this method is eliminating the phase distortion by improved both the hologram recording system and the reconstruction algorithm, which greatly reduced the complicate degree of phase reconstruction process because of cutting the step of phase compensation, and contributes to the on-line detection and fast reconstruction of objects.