In a digital holographic microscopy (DHM) system, different microscope objectives (MOs) will introduce different phase distortions and thus lead to measurement errors. To address this problem, we present a simple and flexible method to compensate all phase distortions by introducing an electrically tunable lens (ETL) in the reference arm for a DHM system with multiple MOs. By exactly controlling the external currents of the ETL, we can change the reference wave front to match the wave front introduced by different MOs without complex alignment or additional numerical postprocessing manipulations. This method is suitable for quantitative real-time phase imaging especially when it refers to multiple MOs. To demonstrate the validity and effectiveness of our scheme, we did a series of simulations and carried out some real experiments with two different MOs (4× and 10×).