Magnetic encoders are widely used in motor drive systems. The existence of harmonic greatly reduces the accuracy of angle demodulation. Based on the angle tracking algorithm of the dual synchronous reference frame-based phase-locked loop (DSRF-PLL), this article proposes a harmonic suppression double synchronous reference frame phase-locked loop algorithm (HS-DSRF-PLL) to solve the harmonic problem in the magnetic encoder. First, the principle of eliminating errors in double synchronous reference frame is studied, and the defects of compensating harmonic errors are pointed out. Then, the harmonic component can be reconstructed on the basis of the reconstructed first harmonic component. The reconstructed harmonic component can be fed back to the signal input terminal and subtracted, which can reduce the influence of the harmonic on the angle calculation. Finally, the simulation and verification are carried out and the proposed harmonic elimination algorithm is realized by the experimental platform. The simulation and experimental results show that the scheme can effectively suppress the influence of the specified harmonic on the angle demodulation.