High-temperature superconducting (HTS) pinning maglev has the potential to achieve high operational speed while having a low maintenance cost, attracting a lot of attention. The HTS pinning maglev system realizes the levitation of the vehicle through the flux pinning characteristics between the high-temperature superconducting bulk and the magnetic field of the permanent magnet guideway (PMG). Thus, the profile of the magnetic field of the PMG can significantly affect the levitation status of the vehicle, which makes the PMG irregularity become one of the main excitation sources of the system. The magnetic induction intensity on the surface of the PMG can be used to characterize the PMG irregularity, but the non-contact dynamic measurement may produce large errors by the vibration of the measurement system during the process. In order to evaluate the PMG irregularity, the vibration component needs to be separated from the overall signal. In this paper, through the synchronous measurement of the Hall sensor and accelerometer, the vibration separation method of the PMG irregularity measurement is simplified to the optimal filter estimation. The particle swarm optimization (PSO) algorithm is used to calculate the parameters of the optimal filter based on the correlation coefficient criterion. The effectiveness of the proposed method is verified by the test. The separated signal is more accurate in both time domain and frequency domain for the characterization of PMG irregularity.