With the increase of the coupling degree of secondary system components in smart substation, it is more and more difficult to evaluate the operation state of system functions and diagnose the fault of secondary system. In this paper, a diagnosis method based on secondary function correlation is proposed. And a function correlation library of secondary system including physical ports is established. The real function information and standard information of function correlation library are matched online by DTW method to complete the fault diagnosis of secondary system. Aiming at the failure of optical fiber link, the physical port mapping can be combined to locate the specific optical fiber at the scene. At the same time, the optical power prediction model is also established, which can warn the optical link communication condition before the failure occurs, and the function affected by the link is given. Finally, the feasibility of the proposed method is verified by the cases appearing in the actual commissioning of smart substations.