In order to correct phase aberrations in the digital holographic microscopy measurement system, a numerical method combined with physical method, namely reference lens method is applied in off-axis digital holographic microscopy system. Firstly, the frequency spectrum of digital hologram is analyzed. By filtering and displacing a part of spectrum, the first-order phase aberration is corrected. Then, the reference lens is introduced in reference path. The axial best position of reference lens is discriminated according to the spectrum center energy. By using this physical method, high-order phase aberration is corrected. Based on the analysis of the phase correction theory, the validity and accuracy of the reference lens method is verified by the combined experiment. The experimental results show that the method of reference lens can accurately correct phase aberration. The standard deviation can reach 0.8 nm. And the measured results agree with measurement results of mechanical profiler, showing that reference lens method can effectively and accurately correct phase aberration of off-axis digital holographic microscopy system.