With regard to the technical features of digital substations， such as the structure， data and information flows， a root cause analysis（RCA） based approach is presented to build the fault diagnosis model for digital substations with the fishbone diagram employed. Based on the logic relationship between the parent node and child node such as the transformer/circuit breaker/transmission line， as well as that between the child cause and root cause in the diagnosis model， the well-developed Dempster-Shafer（D-S） evidence theory is used to integrate different kinds of fault information so as to implement a hierarchical and structured comprehensive diagnosis. An actual fault scenario is served for demonstrating the developed approach for the fault diagnosis problem in digital substations with malfunctions of protective relays and/or circuit breakers， as well as missing and false alarms.