Quantum bit error rate(QBER)of the quantum key distribution system based on the unbalanced Mach-Zehnder interferometer is theoretically analyzed. The influence of the unsymmetry of the two Mach-Zehnder interferometers,the birefringence in the fiber and the fluctuation of the temperature,on the QBER have been discussed in detail. The analytical expression of the QBER is deduced. It shows that the QBER caused by the unsymmetry of the two Mach-Zehnder interferometers defers to the Gauss distribution,QBER caused by the birefringence in the fiber which results in the disaccord of the polarization of the two pulses defers to the cosine distribution,and the fluctuation of the temperature exert great influence on the QBER.