The quantum bit error rate (QBER) caused by time jitter in the phase-coding quantum key distribution (QKD) system is analysed. The physical model of the relation between the QBER and the time jitter in the phase-coding QKD is proposed. The formula between the general waveform function of the single photon pulses and QBER is given. Based on the distribution of Gaussian pulse, the quantitative relation among QBER, the pulse width and the distribution of the time jitter is educed, based on which the QBER of a certain time jitter distribution can be calculated in the Gaussian single photon pulse. The method of reducing the QBER by the control of the system′s time jitter and the width of single photon pulse is proposed.