Abstract: Mobile IPv6 is a protocol proposed by IETF which allows mobile nodes to remain reachable while moving around in the IPv6 Internet. Handover is a key factor that influences Mobile IPv6 performance. Handover latency is too long for real-time application such as VoIP and causes performance degradation of current communication. A network layer handover procedure can be divided into four phases: movement detection, address configuration, home agent registration and correspondent node registration. The impact of different protocol layers and bottleneck of performance in all procedures during handover of MIPv6 is analyzed in this paper based on the experiments of performance measurement. A performance measurement method is deployed to accurately parse delay times in each handover procedure and the modified method of measuring the movement detection delay and the suggestion of reducing the delay in each phase of handover procedure are proposed. By measuring the TCP sliding window and the performance of upper layer applications such as FTP application during handover, the effect of TCP features and performance of upper layer applications in handover procedure are also analyzed. All of these results could provide valuable guideline for improving the performance of mobile handover and designing an effective mobile protocol.