With distributed systems widely used in manufacturing and real-time control of industrial, medical, power, etc. The demand for clock synchronization system becomes urgent. Traditional synchronous mode, such as GPS, NTP, etc., due to the reasons of cost or synchronization accuracy is difficult to meet the demand for industrial applications. Hardware-assisted IEEE1588 clock synchronization technology can greatly reduce the synchronization error. It is the effective way to achieve high-precision synchronization, and lower overall costs. The functional structure of physical layer chip LM3S9B96 and the basic synchronous principle for IEEE1588 protocol are analyzed in this paper. Realized the IEEE1588 clock synchronization module based on LM3S9B96. Testing and validation in LAN, its synchronization accuracy can be achieved nanoseconds.