The invention discloses a fault diagnosis method for a secondary circuit of an intelligent substation. The fault diagnosis method comprises the steps that a mapping relationship between a logical linkand a physical (optical fiber) link is established, and intelligent diagnosis of faults of the secondary circuit is achieved by using link breaking alarm information, protection device and switch port status information, the report control block status sent by a network analyzer and the like. The fault diagnosis method has the beneficial effects that a current secondary circuit diagnosis method mostly relies on the station control layer link alarm information to perform single diagnosis on the logical link fault, and once link breaking occurs, a fault point cannot be quickly analyzed and located from the numerous alarm information; the method combines the link alarm information, port light intensity information, the report control block status and the like, realizes the intelligent diagnosis of the faults of the secondary circuit through multi-source data fusion, and graphically displays the relationship and status between objects of the secondary circuit, thereby providing an efficient and convenient means for intelligent substation secondary circuit abnormity handling and improving the operation and maintenance management level of the intelligent substation.