The invention discloses a transformer station secondary side electric energy measuring system comprising a voltage transformer, a current transformer, a first optical transmitter, a second optical transmitter, a first optical receiver, a second optical receiver, a merging unit, an optical Ethernet switch, an electric energy meter, a computation control center, a clock synchronization module, and a wireless communication module. The transformer station secondary side electric energy measuring system solves a problem that an intelligent transformer station merging unit is long in distance and unsafe in field detection, may synchronously measure electric energy of merging units distributed at different sites and branch electric energy meters, achieves accurate measured values and maintains synchronization, enhances the electric energy metering accuracy and reliability of the transformer station, and is convenient, concise, efficient, and safe.