The invention discloses a three-level bypass control system applied to a secondary reheating unit and a control method of the three-level bypass control system. The secondary reheating unit comprises a boiler, a superheater, a primary reheater, a secondary reheater and a condenser. The three-level bypass control system comprises a high-pressure bypass, a middle-pressure bypass and a low-pressure bypass, wherein the high-pressure bypass is in fluid communication with the superheater and the primary reheater; the middle-pressure bypass is in fluid communication with the primary reheater and the secondary reheater; the low-pressure bypass is in fluid communication with the secondary reheater and the condenser, and therefore different operation modes of the high-pressure bypass or the middle-pressure bypass or the low-pressure bypass can be started when triggering conditions of the high-pressure bypass or the middle-pressure bypass or the low-pressure bypass are satisfied. According to the three-level bypass control system applied to the secondary reheating unit and the control method of the three-level bypass control system, the operation safe reliability of the secondary reheating unit can be greatly improved.