The invention belongs to the technical field of flue gas denitrification and relates to a low-temperature operation prevention automatic protecting method and control system for a flue gas denitrification catalyst. The low-temperature operation prevention automatic protecting method for the flue gas denitrification catalyst comprises the steps that S1, the critical temperature (please refer to the specification) is preset in a distribution control system (DCS); S2, a temperature sensor detects the flue gas temperature Q in a flue in real time and has an access to the DCS; S3, the DCS counts up the continuous operation time A of the condition of MIT