A fault tree automatic forming method and system based on configuration files are provided; the method comprises the following steps: obtaining a SCD file of an intelligent substation; building operation state warning top level events of protection equipment selected in the SCD file; determining a protection equipment operation state warning intermediate event according to the warning top level events and a logic structure in the SCD file of the intelligent substation; building the basic events of the protection equipment operation state according to the protection equipment warning information submitted in a station control level; building the protection system fault tree according to the protection equipment operation state warning top level events, the protection equipment operation state warning intermediate event and basic events. The method and system can automatically form the protection system fault tree according to the intelligent substation configuration file SCD, thus realizing online assessment of the protection equipment real time operation states.