A linear motor is an actuator that has strong thrust and high controllability, and can perform linear motion without the use of a motion converter. In this study, we propose a new method to measure the position of the mover of a permanent magnet linear synchronous motor by measuring the magnetic flux density. To resolve the problem that existing methods have to spatially arrange multiple sensors, the proposed method uses a two-dimensional magnetic flux density measurement value at one point. In accordance with this, the estimation method was modified, the convergence condition of the estimation method was obtained, and the time required for the calculation was estimated. The validity of the proposed method was verified through comparative experiments with existing methods. As a result of the test, the proposed method had a small maximum absolute error compared to the existing methods, and was robust against sensor gain changes.