White light phase-shifting interferometry (WLPSI) has obvious advantages such as large field of view, high precision and non-contact, so it is widely used in three-dimensional (3-D) topography measurement of micro-nano photoelectric devices. In this paper, the problems for large phase unwrapping error and low phase calculation accuracy under the scanning error of piezoelectric transducer (PZT) in current phase shifting measurement are studied. The novel and effective phase-shifting measurement method under scanning error is proposed. This method can be used to accurately recover the surface phase and complete the surface reconstruction under random scanning error with maximum for 10nm. Finally, the proposed method is verified by simulation and measurement experiments.