A controlled atmosphere storage system which is so arranged that a refrigerator and a carbon dioxide generator are connected to each other, and a purifying catalyst, an air preheater, a cooler, a circulating blower and a scrubber are disposed at the downstream side in that order, with the scrubber and the refrigerator being connected, whereby time required for stabilization of combustion may be reduced as compared with conventional systems, and combustion under a low oxygen concentration can be maintained, while flow-out of controlled atmosphere gas outside the refrigerator or entry of atmosphere into the refrigerator can be prevented. Moreover, by forming the carbon dioxide generator in a double wall construction to fill a space with air containing carbon dioxide, heat insulating property is improved for facilitation of combustion under a lower oxygen concentration than in the conventional systems. Furthermore, at starting, since combustion is effected through employment of suction and exhaust paths different from the circulating path, pipe walls are protected against corrosion, and re-ignition under a low oxygen concentration is made possible.