The winding segmented permanent magnet linear synchronous motor has restrictions on the last absolute position acquisition when the power goes from off to on, and the traditional absolute position acquisition systems depend on complex battery and calibration systems. Therefore, a true absolute magnetic encoder based on the Vernier principle with error rejection and decoding technology is studied in this paper. First, the output signal of the magnetic encoder with noise was subjected to the adaptive ellipse parameter correction algorithm with recursive least squares (RLS), and the source output signal predicted and reconstructed. Furthermore, the RLS was optimized by the speed weighting factor and the forgetting factor to reduce the computational pressure and the iterative process. Second, one improved double second-order generalized integrator(DSOGI) decoding technology was investigated by extracting and separating the symmetric-positive sequence components in the unbalanced signal, and, using the phase-locked loop technique for tracking calculation, accurate speed and angle obtained. The adaptive ellipse parameter fitting algorithm effectively reduced the problem of overshoot and steady-state error of the DSOGI, which provides a practical and theoretical basis for the future application of the magnetic encoder. This trajectory arrangement not only avoids the influence of accumulated error on the accuracy of encoder, but it also solves the contradiction between high resolution and small volume, and the advantages over the special decoding chip IC-Haus were also verified by comprehensive experimental results.