The quality of sampling synchronization in the merging unit directly influences the reliability of supervision and protection equipments in a smart substation.According to the correlative technical demand and actual problems of the merging unit，an optimization method which strictly ensures equal-interval sampling control and synchronization is proposed.This method corrects synchronous sampling cycle by measuring the synchronization error in real time，and dynamically compensates for the deviation of local sampling moment based on ensured well-distributed and equal sampling cycle to realize precise sampling moment and synchronization.The test results of sampling synchronization performance show that equal-interval sampling synchronization in the merging unit can be reliably implemented using this technology.