Small phase shift errors in phase-shifting digital holographic microscopy can cause distinct errors in wave-front reconstruction. Phase shift errors generally fall into two categories: numerical errors and uneven errors. A considerable numerical error results from miscalibration of phase shifter and ambient vibrations. Therefore, self-calibration phase-shifting scheme is worth trying. Here, a carrier frequency analysis based self-calibration phase-shifting digital holographic microscopy (PSDHM) is proposed. The actual phase shifts are calculated from Fourier analysis of holograms. The uneven errors are caused by irrational configuration of interferometer. We propose an improved Linik interferometer based setup of phase-shifting digital holography. The experimental results certify that both the self-calibration phase-shifting scheme and the proposed experimental setup have a better reconstruction quality.