The invention discloses a low temperature flue gas SCR denitration system and a working method thereof. An outlet of a fan is divided into two paths; one of the paths is connected to a combustion device on a combustion chamber via a secondary air flow regulating device, and the other path is communicated with a temperature regulating air nozzle in the combustion chamber by a temperature regulatingair flow regulating device, an outlet of the combustion chamber is communicated with a high temperature flue gas injection device in an SCR inlet flue by a high temperature flue gas output pipeline,a combustible gas pipeline is communicated with the combustion device on the combustion chamber, the flammable gas pipeline is provided with a flammable gas flow regulating device, the high temperature flue gas output pipeline is provided with a high temperature flue gas temperature measuring device for detecting flue gas temperature in the high temperature flue gas output pipeline, an outlet on the SCR inlet flue is provided with mixed flue gas temperature measuring device, an outlet of the SCR inlet flue is connected with an SCR reactor, and a low temperature flue gas pipeline is communicated with an inlet of the SCR inlet flue. The system and the working method thereof can realize SCR denitrification treatment on low temperature flue gas. .