The high frequency (HF) square-wave injection sensorless algorithm uses saliency to estimate the motor position affected by the inductance. The structure of the permanent magnets will affect the inductance of the motor, then affect the position estimation performance of the sensorless algorithm. This paper studies the relationship between the inductance and the position estimation accuracy of the HF square-wave injection sensorless algorithm for tubular permanent magnet synchronous linear motor (TPMSLM). Through the finite element simulation, the distribution law of the TPMSLM inductance with the change of the PM structure is quantitatively analyzed, and the influence of the PM structure parameters on the differential amplitude of the HF current is given. The HF square-wave voltage is injected into the stationary reference frame, and the frequency is half of the PWM switching frequency. The HF current differential equation is obtained without any filter, and the estimated position of the mover is extracted by a phase-locked loop. Finally, the experiment of sensorless position estimation is carried out by two prototypes with different PM structure parameters at different speeds, verifying the effectiveness of the analysis.