We measured the surface flatness of both sides for refractive media using the transmitted digital holography method. To enhance the accuracy of the result, phase-shifting system was used. With two different phase modulation of reference beam, the phase profile of object can be easily obtained. Thus, we proposed the surface measurement method which can measure large area fast, compared with conventional methods. To guarantee the reliability of obtained result, we compared with Zygo measurement system. With the proposed method, the surface flatness of 3.45μm resolution could be obtained.