Clock synchronization is a crucial issue for scalable and accurate network performance measurements, especially when no external time sources are introduced. The paper presents a clustering based efficient and robust algorithm Optimized Top-Down Time series Segmentation (OTDTS) for clock synchronization between end-to-end systems. The computational complexity of OTDTS is of order OðKN2Þ. Based on the one-way probe delay traces, the algorithm segments the delay time series at proper points, at which clock dynamics occur. End systems could achieve relative clock synchronization by estimating and removing the clock skew of each segment. Simulations on artificial data set and practical Internet measurement illustrate the availability and efficiency of OTDTS.