Cogging force is a main factor that affects the performance of permanent magnetic brushless DC linear motors (PMBLDCLM) at low speed. Since the cogging force cannot be eliminated thoroughly by design method, compensation must be introduced in the control system. Theoretical analysis of an ideal motor control system with cogging force being considered shows that cogging force can be diminished through a position feedback loop. The finite element analysis (FEA) results prove that the thrust fluctuation of the motor at low speed is mainly caused by cogging force and can be compensated for through position feedback control algorithm. A method of dividing a fundamental circle of the cogging force into sections and performing linear compensation at each section is proposed. Since this method does not need any high precision locating equipments and complicated algorithms, it is easy to be implemented. Experiment results show that the motor thrust fluctuation can be diminished effectively with the method proposed.