The invention relates to a system for using coal-fired and oil-fired boiler flue gas for controlled atmosphere storage and an allocating method of the system. The system comprises waste heat recovery equipment, a flue gas nearly-zero-emission processing system, an N2 and CO2 separation and extraction system, flue gas drying equipment, gas storing equipment and an air filter. The temperature of gas for controlled atmosphere storage is equal to the normal temperature, the temperature of the original flue gas is generally about 150 DEG C, and an approximate 130 DEG C temperature difference between the temperature of the gas and the temperature of the original flue gas needs to be consumed or used. According to the system and the allocating method, waste heat in the flue gas is recovered firstly, so that the energy utilization rate is increased; then flue gas zero-emission processing is carried out on the flue gas, and most of the flue gas subjected to flue gas zero-emission processing is further subjected to carbon dioxide separation or drying treatment and enters the corresponding gas storing equipment to be stored; thus, the flue gas and air are matched for keeping freshness of stored articles in a storage room, and the flue gas is effectively used; besides, no independent inert gas generation equipment needs to be arranged, the regulating range of controlled atmosphere gas components is widened, and the operation cost of controlled atmosphere storage is remarkably reduced.