PURPOSE: To provide a method and system therefor designed to prevent air pollution due to the mass release of a pest-controlling gas and also ensure pests living among stored grains to be exterminated by the use of relatively small amounts of the gas.

CONSTITUTION: A vacuum vessel 2 is first filled with stored grains 18 and the inside of the vessel 2 is kept at a specified degree of vacuum to cool both the grains 3-8 and pests living among them. Secondly, a high-pressure pest- controlling gas such as carbon dioxide is introduced into the vessel 2 and made to selectively absorb into the pests by making use of moisture content difference to effect extermination or deactivation of the pests. Then, the grains 18 are fed into a large-sized vacuum vessel 9 and the pests are ground by making use of the abrupt expansion of the pest-controlling gas such as carbon dioxide.