This paper proposes a phase-shifting digital holographic microscopy (PSDHM) for microstructure measurement by sweeping the repetition rate of femtosecond laser, and a multiple reflection arrangement between two quasi-parallel mirrors is constructed for optical multiplication. High precision phase-shifting can be achieved by sweeping the repetition rate of the femtosecond laser referenced to a Rb atomic clock without any mechanical sweeping. Optical multiplication can shorten the spatial distance of the optical delay line used for pulses alignment, make the PSDHM structure compact and stable, and avoid certain environmental disturbances. In the experiments, a ten-step phase-shifting test was first carried out for evaluating the phase-shifting accuracy, and the phase-shifting error was calculated to be in the range of −1° to 0.25°. Then, a USAF 1951 resolution target and a microstructure standard target were measured using a four-step PSDHM, and the measurement results were compared with those from a stylus profiler and a white light interferometer, respectively. The lateral resolution of PSDHM was tested to be about 2.1 μm, and the maximum error of the longitudinal measurement was within 6 nm. Experiments verify that the PSDHM system has good performance in terms of phase-shifting accuracy, surface topography measurement and coherent noise suppression.