The invention discloses an electric control engine idling operation in-gear flameout system and a control method thereof. The system comprises an engine controller, a temperature sensor and an idling in-gear flameout control system, wherein the input end of the temperature sensor is connected with the input end of the engine controller through a first temperature signal input bundle and a second temperature signal input bundle. The electric control engine idling operation in-gear flameout system designs an oil injection limiting strategy during forced idling operation of an engine, by means of an electric control system heat protection oil limiting principle, the system is used for manually limiting heat protection oil quantity by the oil injection characteristics of fuel oil during starting operation of a vehicle and carrying out different settings aiming at a vehicle air-conditioning device, so that corresponding power output of the engine during starting of the vehicle is avoided, and therefore the goal of flameout of the vehicle during mistaken in-gear is achieved, the precision and the sensitivity of the system are high, the occurrence of peril accidents can be avoided, and the control cost is low.