A phase-contrast imaging technology with digital holographic microscope based on system calibration is present. After a theoretical analysis of the phase-contrast microscopy,results show that the phase curvature introduced by the microscope objectives can be compensated by introducing two digital phase masks located on recording plane and imaging plane respectively. Without affecting the sice of the reconstructed image,the mathematic models of the two phase masks are defined,which can be constructed by the proposed system calibration method. The calibration process includes pre-recording two reference holograms,inserting the imaging microscope objective,filtering and square fitting etc digital processing to compute the recording system parameters,constructing the required digital phase masks by the calibrated system parameters. Finally,a demonstration experiment is carried out. In the experiment a small water bead with size of no more than 0.09 mm is phase-contrast imaged with different magnification ratios. The experiment shows that the proposed method is credible and convenient.