Aiming at the problem of clock frequency drift in IEEE1588 clock synchronization process, a novel clock synchronization algorithm based on sliding mode control is proposed. Firstly, the state space model of the system is established according to the recurrence relationship between master-slave clock offset and drift. Then, the sliding mode control is used to reduce the clock skew and clock drift. Finally, the frequency jitter and random error in the experimental process are optimized by sliding average filter. The results show that the clock synchronization algorithm based on sliding mode control can effectively restrain the linear growth of clock skew caused by clock drift, and control the clock skew below 1 μs, thus, realizing sub microsecond network time synchronization. Compared with the traditional IEEE1588 protocol synchronization method, the proposed method provides higher synchronization accuracy.