As a widely used motor rotor position measuring device, the measuring accuracy of the magnetic encoder has an important impact on the performance of the entire control system. In order to improve the measuring accuracy of rotor position, the dual second-order generalized integrator with phase-locked loop (DSOGI-PLL) decoding algorithm is used to extract the positive sequence components of the output signals of the magnetic encoder, and restrain the amplitude error and phase error in the output signals of the magnetic encoder. Aiming at the defect that the conventional second-order generalized integrator (SOGI) cannot suppress the DC offset error, the improved second-order generalized integrator (ISOGI) is proposed to eliminate the DC offset error and improve the decoding accuracy of the magnetic encoder. The simulation and experiment results verify the effectiveness of the proposed method.