The invention relates to a comprehensive automation integrated protecting method and a system which adopt an integrated IED to carry out automation functions such as protection, measurement and control, computation and the like of all bay units in a substation; state quantity, analog quantity and digital quantity which are output in interval by primary equipment on a process layer of the substation are respectively uploaded to the integrated IED through an ethernet switcher by a dual Ethernet (100mega/1000mega), and the protection and automation function of the substation are realized by calculating and processing the state quantity, analog quantity and digital quantity which are output in interval respectively by the integrated IED, therefore, a spacing layer and a substation layer of the substation are unified into one layer according to IEC61850 standard, and a plurality of IEDs are integrated into one integrated protecting IED, and two same integrated IEDs are provided for hot spare for improving the reliability. The comprehensive automation integrated protecting system leads the substation integrated protecting functions to share a uniform information platform, and communication network is used for replacing control cables, thus improving the reliability of the signal transmission, further improving automation and management level and reducing comprehensive construction cost.