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Since organic rice storage silos were faced with an insect problem, an owner solved this problem using the expert system (ES) in the controlled atmosphere process (CAP) under the required standard, fumigating insects with an N2, reducing O2 concentration to less than 2% for 21 days. This article presents the computational fluid dynamics (CFD) assisted ES successfully solved this problem. First, CFD was employed to determine the gas flow pattern, O2 concentration, proper operating conditions, and a correction factor (K) of silos. As expected, CFD results were consistent with the experimental results and theory, assuring the CFD’s credibility. Significantly, CFD results revealed that the ES controlled N2 distribution throughout the silos and effectively reduced O2 concentration to meet the requirement. Next, the ES was developed based on the inference engine assisted by CFD results and the sweep-through purging principle, and it was implemented in the CAP. Last, the experiments evaluated CAP’s efficacy in controlling O2 concentration and insect extermination in the actual silos. The experimental results and owner’s feedback confirmed the excellent efficacy of ES implementation; therefore, the CAP is effective and practical. The novel aspect of this research is a CFD methodology to create the inference engine and the ES.