Optical pulse will reach the receiver not at exact time instance due to the transmission through the long trunk fiber, and this phenomenon will effect on the bits error rate in the Quantum key distribution (QKD) system to some extend. The time jitter based on the differential phase shift quantum key distribution system and two asymmetric Mach-Zehnder interferometers is measured outdoors in different transmission distance and the physical model of the relationship between the time jitter and the quantum bit error rate is proposed. According to this relationship, the quantum bit error rate can be estimated for some optical pulse shape and some statistical distribution function.