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With the application in smart substation with the IEC 61850 standard, the time synchronous precision requirement to the IED (Intelligent Electronic Device) reaches T5 grade (1us), and the time synchronous precision using IEEE1588 technology can meet the T5 grade. This paper firstly introduces the principle of IEEE 1588 standard, and then describes the function of the PTP925d clock module. The test data analysis using the PTP925d clock module proves that the time synchronous precision of IEEE1588 assisted by hardware reaches nanosecond grade. The function structure of the smart substation using IEC61850 standard is analysis. Then the project design of PTP time synchronization in and among smart substations is made using the PTP925d clock module, and the technique details are narrated to refer to the engineering application for IEEE1588 standard in smart substation.