The invention discloses intelligent substation secondary optical fiber loops, and a safety isolation system and an isolation method for the intelligent substation secondary optical fiber loops. The intelligent substation secondary optical fiber loops, the safety isolation system and the isolation method belong to the field of intelligent substation relay protection. A relay protection device is connected with an intelligent terminal, a process layer switch and a merging unit in series separately via optical cables, so as to form the secondary optical fiber loops. An optical fiber connecting device is connected in each of the three secondary optical fiber loops in series for setting a breakpoint for optical path splitting and merging operations, and a process layer monitoring module is connected in each secondary optical fiber loop in series for monitoring real-time information of the secondary optical fiber loop so as to judge reliable switching-off and reliable restoration of the secondary loop. The safety isolation system and the isolation method can be used for performing safety isolation on the secondary optical fiber loops, effectively solve the problems that an intelligent substation is lack of physical isolation and has hidden danger of unreliability, are convenient for the operation and maintenance staff to perform safety measure operation and monitoring on the secondary loops, reduce the safety isolation risk of the intelligent substation secondary optical fiber loops, and improves safety and reliability of operation and maintenance of the intelligent substation.