The ordinary synchronization mode in distributed Ethernet network shows low synchronization accuracy and complex network construction, so this paper introduces IEEE1588 clock synchronization protocol to the Ethernet network in smart substation. Calibration characteristics and clock attribute of the IEEE1588 common clock, boundary clock and transparent clock model are analyzed, and the simulation model of network structure of smart substation is built to conduct model verification and calibration characteristic simulation test. Results show that the IEEE1588 protocol used in Ethernet smart substation improves the precision of clock synchronization, simplifies the network structure of smart substation, and has practical value of popularization and application.