The performance of sensorless control in a permanent magnet synchronous machine (PMSM) highly depends on the accuracy of rotor position estimation. Owing to its strong robustness, phase-locked loop (PLL) is widely used in rotor position estimation. However, due to the influence of harmonics existing in back electromotive force (EMF), estimation error occurs by using PLL. In this paper, a hybrid filtering stage-based PLL is proposed to improve the rotor position estimation. Adaptive notch filters and moving average filters are integrated together to eliminate harmonic EMF. To make the method effective under varying speed conditions, adaptive parameters design guidelines are provided, considering dynamic performance under a wide operating range. The proposed method can accurately detect rotor position even under harmonic EMF disturbances. It can also adjust the frequency adaptively based on the rotating speed of the rotor, which means the estimation performance is not deteriorated under rotating speed changing conditions. The simulation results verify the effectiveness of the proposed method.