Dead-time effect results in distorted currents and force pulsations of Permanent Magnetic Linear Synchronous Motors(PMLSM), which limits the uses of precision stages in conditions of high accuracy, low frequency and lighter loadings. To compensate the Dead-time effect, this paper proposed a Double Updating Dead-time Compensation (DUDTC) method to correct each input pulse width of the motor driver according to phase current polarity. Firstly, the effect of dead-time on driver output pulses was analyzed and the correlation between correction of Pulse Width Modulation(PWM) and phase current polarities was given. Then, the method was evaluated through simulations in Matlab/Simulink and experiments in a linear-stage system. The results indicate that the phase error of DUDTC is only 0.5 servo periods and its phase current distortions is reduced. The DUDTC shows less codes and good portability, and is an efficient method to compensate the dead-time effect in digital drive systems.