This paper expounds the system structure of the sampled value transmit by network in smart substation, analyses time sequence of electronic instrument transformer sampled value transmit by network and key technologies of sample synchronization, based on this, puts forward a kind of longitudinal optical differential synchronization scheme based on the sampled value transmit by network. Using this scheme the optical differential sample synchronization is completed in merge unit, the opposite data based on calculated sampling time deviation of two sides and the time resample stamp of this side are resampled, finally sample synchronization is finished in the merge unit, and then the synchronous sampled value is sent to the network by IEC61850-9-2. Theoretical analysis and simulation results prove that the sample synchronization scheme does not rely on the source synchronous clock, and has advantages of high precision, small burden, being easy to carry out, and the flexible engineering application and strong compatibility, so it has widely practical significance.