The invention relates to an IEEE1588 clock synchronization method based on a disturbance observation control technology. According to a feedback control method based on extension state observer, a state space model of a frequency compensation clock is established; uncertain factors like a crystal oscillator frequency drift and a time stamp quantification error that affect the clock synchronization precision come down to ''sum disturbance'' and are extended into new state variables; estimation is carried out by using the extension state observer and a frequency compensation value is calculated by designing a feedback control law; and a slave clock adjusts the frequency according to the frequency compensation value, so that an objective of synchronization of a master clock and a slave clock is achieved. Therefore, the precision and stability of clock synchronization can be improved obviously.