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Permanent magnet linear motors are a type of linear motors that are generally used in precision motion control applications. However, the position of motor is easily disturbed by external force, disturbance, and variation in parameters of plant. Therefore, the construction of the high-precision linear motion system is a difficult task. This paper implements a modified disturbance observer and compensator, which includes a novel variable gain, to overcome the effects of unknown parameters of the motor, to minimize the effect of the disturbance, and to reduce the response time of the disturbance. This compensated linear motor is further controlled by the internal model reference control algorithm so that the position of the motor can be tracked with expected response precisely. The authors conducted the experiments and verified the feasibility of the high-precision positioning control. Compared with the case of normal disturbance compensator, the experimental results also illustrate the improvements of the novel variable gain, which reduces the response time toward the command signal and the external disturbance.