The fourth-generation synchrotron radiation light source under construction has a higher requirement for alignment measurement than former-generation light sources, including the accuracies and efficiencies. In this paper, a robust smoothing analysis strategy that aims to reduce relative position errors is introduced to smooth the magnetic centers’ orbit. First, we pre-process the original data based on gross error detection. Then, we do a smooth analysis of the data of the magnetic centers’ orbit and iteration by using the curve fitting of the Parzen-window function. Finally, the physical accelerator calculation is utilized to terminate the iteration. Simulation results based on the Hefei Advanced Light Facility show that the comparison between the physical calculation results before and after using this strategy verifies that it can dramatically improve beam quality, which has a slight improvement concerning existing methods. Besides, this strategy requires lower quantities of magnets that need to be adjusted, less than that of other methods. This research can provide a robust technical guarantee for the construction of the fourth-generation light source.