In order to meet the requirements of real-time behavior correctness and certainty of safety critical real-time embedded system, the paper shows a design and implementation of clock synchronization system with hardware timestamp characteristics of the of ETSEC Ethernet device controller. The real-time embedded operating system ReWorks and IEEE 1588 precision clock synchronization protocol is adopted for the implementation. The synchronization accuracy is less than 100 ns, and the accuracy and precision of the clock synchronization system are tested and verified.