The invention relates to an application function linkage rule verification method and a system for an intelligent substation. An advanced application function testing system enables the sequence control module of a to-be-tested advanced function application system to send the sequence control information to a process layer and an interval layer simulation IED of the intelligent substation. The advanced application function testing system acquires the sequence control feedback information from the process layer and the interval layer simulation IED of the intelligent substation. The advanced application function testing system enables an intelligent alarm module of the to-be-tested advanced function application system to send the alarm information according to the sequence control feedbackinformation, compares the alarm information with the alarm information of the same type pre-stored in an advanced application function case verification database, and verifies the linkage accuracy ofthe alarm information. According to the invention, the detection is carried out through the advanced application function linkage rule detection, the accuracy comparison and analysis and other means for the intelligent substation. Therefore, the labor cost and the material cost of the advanced application function linkage rule detection of the intelligent substation are saved.