The invention relates to an application data switching method and system for an area protection control system. The method and the system are used for obtaining sampling data based on satellite time service and sampling data based on network time service on the basis of double time scales carried in network sampling data, namely a corresponding absolute satellite time scale of local satellite time service and a network main clock absolute time scale of area network main clock uniform time service, carrying out real-time synchronous verification on the sampling data based on satellite time service and sampling data based on network time service, generating data abnormality alarm information according to a real-time synchronous verification result, switching the sampling data that is used for calculating the application data for differential protection of an area substation according to the data abnormality alarm information, identifying abnormal network sampling data when discovering that synchronization abnormality of the sampling data that is used for calculating the application data of the area substation, and seamlessly switching the abnormal network sampling data for calculating the application data to the normal sampling data, so as to ensure the accuracy of the differential protection of the area substation.